Skip to content

Category: microbes

Published on

Considering all the antibiotics that the typical sinusitis sufferer takes over the years, reading this article was depressing. One wonders, can the gut microbiome (community of microbes) recover from many rounds of antibiotics and how long does it take? Please note: CD is Crohn's disease, UC is ulcerative colitis, and IBD is inflammatory bowel disease. Dysbiosis means that the community of microbes (microbiome) is out-of-whack. From Medscape:

Antibiotics Associated With Increased Risk of New-onset Crohn's Disease but not Ulcerative Colitis

The objective of this study was to perform a meta-analysis investigating antibiotic exposure as a risk factor for developing inflammatory bowel disease (IBD).A literature search using Medline, Embase, and Cochrane databases was performed to identify studies providing data on the association between antibiotic use and newly diagnosed IBD. 

Conclusions: Exposure to antibiotics appears to increase the odds of being newly diagnosed with CD but not UC. This risk is most marked in children diagnosed with CD.

--------------------------------------------------------------------------

Environmental factors have a key role in the pathogenesis of inflammatory bowel disease (IBD)...Furthermore, the incidence of IBD has been increasing worldwide over time. Developing countries have seen an increase in IBD incidence as they have Westernized.

Emerging evidence suggests that certain medications are associated with an increased risk of new-onset IBD. In particular, antibiotics have been linked to the development of both Crohn's disease (CD) and ulcerative colitis (UC).Growing research suggests that the microbiome and its interaction with the mucosal immune system are important in the pathogenesis of IBD.Antibiotics can cause alterations to the microbiome that may potentially contribute to the dysbiosis and dysregulated immune response seen in IBD.

Previous studies have investigated the association of antibiotic exposure with newly diagnosed IBD in both adult and pediatric populations. CD has been more consistently associated with antibiotic use, with some studies demonstrating an increased risk of CD but not UC. It also appears that patients who receive more frequent courses of antibiotics have a higher likelihood of developing IBD.

The results of this meta-analysis suggest that exposure to antibiotics increases the risk of new-onset IBD. When stratifying by type of IBD, antibiotic exposure was associated with an increased risk of developing CD but not UC. We found that the magnitude of risk of new CD is greater for children than for adults. All classes of antibiotics studied, with the exception of penicillins, were associated with new diagnoses of IBD. Interestingly, the types of antibiotics showing the strongest association were fluoroquinolones and metronidazole.

Although it is impossible to draw causal links on the basis of these data, there are some possible implications and explanations for our findings. First, our findings may support the importance of disruptions in the microbiome in the pathogenesis of IBD. The link between antibiotic exposure and new IBD seems biologically plausible. It is known that the microbiome likely has an important role in the pathogenesis of IBD. Studies have shown a decrease in the diversity and stability of both mucosa-associated bacteria and fecal bacteria in patients with CD and UC.For example, the largest cohort microbiome study to date recently found that newly diagnosed CD patients have increased Enterobacteriaceae,Pasteurellaceae, Veillonellaceae, and Fusobacteriaceae, and decreased Erysipelotrichales, Bacteroidales, and Clostridiales.

Antibiotics have been shown to alter the composition of the human gut microbiota by decreasing taxonomic richness and diversity....Although the microbiome may recover to its initial state within days to weeks after antibiotic treatment, some studies have shown a longer-term impact of antibiotics on specific microbial populations that can persist for months to years.

It is unclear as to why antibiotic exposure was associated with new-onset CD and not UC. Studies have suggested a difference in the microbiota between CD and UC patients....Our finding that pediatric populations appear to have an increased association of antibiotic use with new-onset CD compared with adults may reflect the less stable nature of the microbiome earlier in life. During the first 3 years of life, the microbiome appears to undergo marked changes and significant maturation toward an adult-like composition with greater interpersonal variation. It is possible that antibiotics may therefore have a greater impact during childhood when the gut microbiota composition is still developing.

Published on

The numbers are amazing. Researchers found all these microbes because of state of the art genetic analysis such as 16S rRNA gene sequencing (because most microbes can not be "cultured"). From Science Daily:

Cataloguing 10 million human gut microbial genes: Unparalleled accomplishment

Over the past several years, research on bacteria in the digestive tract (gut microbiome) has confirmed the major role they play in our health. An international consortium has developed the most complete database of microbial genes ever created. The catalogue features nearly ten million genes and will constitute a reference for all research on gut bacteria.

Research on the gut microbiome (all of the bacteria in the digestive tract) has multiplied over the past several years, helped in great part by new sequencing technologies. The gut microbiome, which scientists have labelled a "new organ" that is composed of tens of trillions of bacteria -- ten times as many as the number of cells in the human body -- is directly linked to the immune system and brain. It is a major player in chronic illnesses such as obesity and Type 2 diabetes. However, research in the field depends on access to reference gene databases (or catalogues), which is particularly important when identifying the functions of microbial genes. Few and far between, existing catalogues were created using samples from a limited number of people and geographical origins.

Most of the genes (around six million) are shared by just 1% of the population, making them quite rare. While there is substantial data today regarding the most common genes, future research will focus on determining the importance and role of these rare genes.

Thanks to this catalogue, the most clinically significant genes can be described, most notably those related to illnesses such as Type 2 diabetes, cirrhosis of the liver, cardiovascular diseases and some cancers. It will also provide a more complete picture of imbalances in the gut microbiome (dysbiosis), particularly those caused by medication.

Published on

Much discussion about the link between gut bacteria and liver cancer, as well as the link between inflammation and cancer. Gut microbiome imbalances can cause health harms.

Bottom line: Try to improve your gut microbiome by eating a diet rich in fruits, vegetables, seeds, nuts, legumes, and whole grains.

From the Dec.4, 2014 issue of Nature: Microbiome: The bacterial tightrope

Imbalances in gut bacteria have been implicated in the progression from liver disease to cancer. The team's research, published last year, suggests that gut bacteria — which are part of the microbiome of bacteria and other microorganisms that live in and on the body — can play a crucial part in liver-cancer progression.

There are trillions of microorganisms in the human microbiome — they outnumber their host's cells by around ten to one — and their exact role in health and disease is only now starting to be explored. Studies have found that people with non-alcoholic fatty liver disease have a different composition of bacteria in their gut from healthy individuals2, 3

 Instead, she sees an emerging picture of liver disease and cancer as a process in which various factors — including a high-fat diet, alcoholism, genetic susceptibility and the microbiome — can each contribute to the progression from minor to severe liver damage, and from severe liver damage to cancer.

Flavell's research suggests that the liver has an important role in immune surveillance and helps to maintain bacterial balance in the gut. Specialized cells in the liver and intestines monitor the microbiome by keeping tabs on bacterial by-products as they pass through. These cells can detect infections and help to fight them.

But they can also pick up on subtler changes in the bacterial populations in the gut. When certain types of bacteria become too numerous — a state called dysbiosis — the immune system becomes activated and triggers inflammation, although at a lower level than it would for an infection... Now, research is emerging that suggests that dysbiosis and the immune reaction it provokes can even contribute to cancer.

He thinks that at least part of this mechanism involves disruption in the balance of the various species of bacteria in the gut. An out-of-balance microbiome promotes a constant state of inflammation, which can contribute to cancer progression, Schwabe says. This aligns with the picture that is emerging of cancer, in general, as an inflammatory process: the same immune reactions that help the body to fight infection and disease can also promote unchecked cell growth.

Some of the earliest research on the human microbiome, published in 2006, demonstrated that the balance of gut bacteria in obese people is different from that in people of healthy weight. In particular, obese people tend to have greater numbers of the bacteria that produce DCA (deoxycholic acid) and other secondary bile acids.

This line of research points to the microbiome as one potential link between obesity and liver-cancer risk . And, much like Schwabe's work, Hara's results indicate that several factors converge to promote cancer: in this case, bacteria, diet and carcinogen exposure. Here, too, the ability to stave off the disease seems to depend on maintaining the appropriate microbial balance. Overweight mice and people have a different composition of gut microbiota from their lighter counterparts, and they have higher levels of DCA, too.

However, not everyone is convinced that individual bacterial species are to blame. Some researchers point out that dysbiosis, and therefore cancer risk, involves multiple strains of bacteria. And the bacterial mix can vary from person to person, meaning it is unlikely that scientists can pin all responsibility on a single species.

Others are looking for ways to promote the growth of healthy bacterial strains rather than target the bad ones....There is also some early clinical evidence that specially formulated probiotics — cocktails of good bacteria — can bump the microbiome back into balance. Hylemon and his colleagues gave people with cirrhosis a probiotic containing Lactobacillus bacteria and found that their blood markers of inflammation decreased along with their cognitive dysfunction (a common symptom of cirrhosis)6. Although the study was not designed to evaluate cancer risk, it does show that delivering bacteria to the gut can have positive therapeutic effects on the liver.

Published on

Please note that the study was of people living in the Baltimore, Maryland area - so it is unknown if this would hold true for people living elsewhere. From Medical Xpress;

Virus may affect mental abilities, study reports

People with an algae virus in their throats had more difficulty completing a mental exercise than healthy people, and more research is needed to understand why, US scientists say. A study in the Proceedings of the National Academy of Sciences showed that the virus was present in about half of 92 human subjects studied, and those who had it performed worse on certain basic tasks.

The virus, known as Acanthocystis turfacea Chlorella virus 1, or ATCV-1, also appeared to limit the cognitive abilities of mice.The mice had a harder time navigating a maze and noticing new objects in their surroundings after they were infected.

It remains unclear if the virus was truly driving the drop in mental functioning. Researchers have not yet shown the cause and effect between the virus and the intelligence results."At this point we do not think that this virus should be considered as a threat to individual or public health," said lead researcher Robert Yolken, a virologist at Johns Hopkins University in Baltimore, Maryland. The virus was found by accident while scientists were analyzing microbes in the throats of healthy humans for a different study.

Experts have been studying viruses similar to ATCV-1 for 35 years, said senior author James Van Etten of the University of Nebraska, an expert on algal viruses. Van Etten joined the research four years ago when Johns Hopkins scientists found ATCV-1's DNA sequences in the brain tissue of people who had died with mental disorders such as schizophrenia.

"These viruses are ubiquitous in fresh water ponds and streams throughout the world," Van Etten said. He noted that the virus—previously thought to only infect algae—could make its way into the human body when people swallow water while swimming.There might also be another host in nature, such as mosquito larvae, he said. But the nature of the disease is still in the early stages of analysis.

It is also unknown if the virus's effects on the brain are lasting or temporary. Scientists have long understood that viruses interact with DNA, and further studies could shed more light on the role of the virus on cognition.

"As more studies like this are conducted, I believe we'll find out there's even more interaction between viruses, bacteria and fungi that are either ingested or breathed into our noses and mouths and the overall human condition," said Jordan Josephson, ear nose and throat specialist at Lenox Hill Hospital in New York, who was not involved in the study.

Further information on this study and the virus. From Medical Xpress:

Researchers identify algae-virus DNA in humans

From Newsweek:

American Researchers Discover 'Stupidity Virus'

Published on

Natural ways that may help GERD symptoms without drugs : eating smaller portions, losing weight, not lying down for 2 hours after eating, and avoiding alcohol, cigarettes, and "trigger" foods.From Health Day News:

Could Popular Heartburn Drugs Upset Your 'Good' Gut Bugs?

Heartburn drugs such as Prilosec and Nexium may disrupt the makeup of bacteria in the digestive system, potentially boosting the risk of infections and other problems, a small new study suggests.

According to Harvard Medical School, billions of dollars are spent annually on antacid drugs in an attempt to combat heartburn, ulcers and gastroesophageal reflux disease, also known as GERD. Old standbys such as Maalox and Mylanta have been supplanted by more effective, more expensive drugs, including proton pump inhibitors. These include Prevacid (lansoprazole) and Protonix (pantoprazole) in addition to Prilosec (omeprazole) and Nexium (esomeprazole).

Long-term use of proton pump inhibitors has been linked to infection with a germ called Clostridium difficile, which causes severe diarrhea, he said. Researchers have also connected the medications to vitamin deficiencies, bone fractures and pneumonia, among other conditions.

In the new study, researchers sought to understand what happens to the trillions of germs in the digestive system when people take omeprazole, the generic name for the drug best known as Prilosec.Ten participants, aged 18 to 57, took 20 or 40 milligrams of the drug a day for 28 days. Researchers analyzed the study participants' stool samples to understand the germs in their guts.

"These microbes have evolved with us to participate in our normal development and metabolism, and perform certain functions that we would not be able to accomplish without their help," DiBaise said. Many scientists believe that people's risk of disease goes up when their normal germ makeup changes, he said.

The researchers found evidence that the medications disrupted the balance of bacteria in the digestive systems of the participants, and the changes lasted for at least a month after they discontinued the drug. It didn't seem to matter whether they took the higher or lower dose, DiBaise said.

DiBaise cautioned that the study doesn't prove that the drug causes users to become more vulnerable to C. difficile infections. However, it shows that the drug "creates a situation in the gut microbial environment that may increase an individual's susceptibility," he said.

What should users do for now? According to DiBaise, proton pump inhibitors are "the most effective medications to treat gastroesophageal reflux disease." If patients don't have the most severe symptoms, he said, other types of heartburn drugs might help. Also recommended: eating smaller portions, losing weight, not lying down for two hours after eating, and avoiding alcohol, cigarettes and "trigger" foods.

Published on

Are probiotic bacteria the reason?

From Medical Xpress: Does a yogurt a day keep diabetes away?

A high intake of yogurt has been found to be associated with a lower risk of developing type 2 diabetes, according to research published in open access journal BMC Medicine. This highlights the importance of having yogurt as part of a healthy diet.

Type 2 diabetes is a chronic condition that occurs when the body doesn't produce enough insulin, or the body's cells develop resistance to insulin. There is an increased risk of developing it if a relative has the condition or if an individual has an unhealthy lifestyle. 

Researchers from Harvard School of Public Health pooled the results of three prospective cohort studies that followed the medical history and lifestyle habits of health professionals. These studies were the Health Professionals' Follow-up Study (HFPS), which included 51,529 US male dentists, pharmacists, vets, osteopathic physicians and podiatrists, aged from 40 to 75 years; Nurses' Health Study (NHS), which began in 1976, and followed 121,700 female US nurses aged from 30 to 55 years; and Nurses' Health Study II (NHS II), which followed 116,671 female US nurses aged from 25 to 42 years beginning in the year 1989.

Within the three cohorts 15,156 cases of type 2 diabetes were identified during the follow-up period. The researchers found that the total dairy consumption had no association with the risk of developing type 2 diabetes. They then looked at consumption of individual dairy products, such as skimmed milk, cheese, whole milk and yogurt. When adjusting for chronic disease risk factors such as age and BMI as well as dietary factors, it was found that high consumption of yogurt was associated with a lower risk of developing type 2 diabetes.

The authors then conducted a meta-analysis, incorporating their results and other published studies, up to March 2013, that investigated the association between dairy products and type 2 diabetes. This found that consumption of one 28g serving of yogurt per day was associated with an 18 per cent lower risk of type 2 diabetes.

Previous research has suggested calcium, magnesium, or specific fatty acids present in dairy products may lower the risk of type 2 diabetes. It has been shown that probiotic bacteria found in yogurt improves fat profiles and antioxidant status in people with type 2 diabetes and the researchers suggest this could have a risk-lowering effect in developing the condition. 

Published on

Amazing persistence of the restroom microbial community.From NPR news:

What Microbes Lurked In The Last Public Restroom You Used?

The invisible world of the bathroom isn't pretty — unless you're a microbe. After scanning the microbial zoo of four public restrooms recently, a team of researchers found a diverse swarm of characters that persisted for months despite regular cleaning of the facilities. The goal of the study, published in the December issue of Applied and Environmental Microbiology, was to better understand how communities of bacteria and viruses can shift in these very public places across a couple of months.

To get their down-and-dirty readings, the researchers selected four bathrooms at San Diego State University... They checked two women's restrooms and two men's restrooms (a high-traffic and a low-traffic bathroom for each gender). The bathrooms were thoroughly cleaned at the study's start with bleach solution, which killed any existing germ communities.Then, during the following hours, days, weeks and months of human use, the researchers periodically swabbed soap dispensers, floors and toilet seats in all four restrooms for microbe samples. 

Within one hour of sterilization, the bathrooms were completely recolonized with microbes — just as plants rapidly arrive and populate a newly emerged island. Fecal bacteria dominated, including on toilet seats and on soap dispensers — about 45 percent of the bacteria there were of fecal origin.

In all, the scientists found genetic traces of more than 77,000 distinct types of bacteria and viruses. (At least some of those species were likely dead or dormant, the scientists add; genetic testing detects them all, whatever their status.)

Patterns of regrowth and succession, as some species waned and others replaced them, were surprisingly similar from bathroom to bathroom; within just five hours the population mix in each room stabilized.

When the team tried growing cultures from different surfaces in each room, they found one set of live bacteria in overwhelming abundance: Staphylococcus. Staph's persistence in these studies points to its power as a potential pathogen, Gilbert says. Various versions are common on human skin and inside the nose and other orifices; they generally cause no problems, or trigger only minor skin infections. But staph infections can be serious, or even kill, if the bacteria get into bloodstream, joints, bones, lungs or heart. 

Gilbert notes that none of the live Staph strains detected in the San Diego bathrooms showed signs of being antibiotic resistant. They were instead relatively harmless "skin bugs that happened to have lost their skin," he says. The team did find genes from MRSA hiding on the floor, as well as traces of some troublemaker viruses, including HPV and herpes virus.

Interestingly, although restrooms that were left open for use for up to two months were cleaned regularly with soap and water, the communities of microbes found there remained relatively unchanged for the full eight weeks of the study.

No need to be scared or grossed out by that finding, Gilbert says..."All human environments contain pathogens — your bedroom, the phone you're talking on, even the bugs inside of you could turn pathogenic at any time," Gilbert tells Shots. "But we desperately need them in our lives." Having a healthy community of good — or even just neutral — microbes can crowd out the bad ones. As we've learned from using broad-spectrum antibiotics in the human body, "sterilization is not necessarily good," he says. "Bacteria come back right away, and they might come back perturbed."

Published on

Amazing how long the bacteria persisted in the air. From Science Daily:

Hand dryers can spread bacteria in public toilets, research finds

Modern hand dryers are much worse than paper towels when it comes to spreading germs, according to new research. Scientists from the University of Leeds have found that high-powered 'jet-air' and warm air hand dryers can spread bacteria in public toilets. Airborne germ counts were 27 times higher around jet air dryers in comparison with the air around paper towel dispensers.

The study shows that both jet and warm air hand dryers spread bacteria into the air and onto users and those nearby.

The research team, led by Professor Mark Wilcox of the School of Medicine, contaminated hands with a harmless type of bacteria called Lactobacillus, which is not normally found in public bathrooms. This was done to mimic hands that have been poorly washed.

Subsequent detection of the Lactobacillus in the air proved that it must have come from the hands during drying. The experts collected air samples around the hand dryers and also at distances of one and two metres away. Air bacterial counts close to jet air dryers were found to be 4.5 times higher than around warm air dryers and 27 times higher compared with the air when using paper towels. Next to the dryers, bacteria persisted in the air well beyond the 15 second hand-drying time, with approximately half (48%) of the Lactobacilli collected more than five minutes after drying ended. Lactobacilli were still detected in the air 15 minutes after hand drying.

Professor Wilcox said: "Next time you dry your hands in a public toilet using an electric hand dryer, you may be spreading bacteria without knowing it. You may also be splattered with 'bugs' from other people's hands.

Published on

Exciting research in a new area - our trillions of viruses or virome. From the new research it looks like some of the viruses are beneficial to us and help keep us healthy. It's time to stop thinking of all viruses (and bacteria) as bad, but instead that some viruses are necessary for good health. From Science Daily:

Natural Gut Viruses Join Bacterial Cousins in Maintaining Health and Fighting Infections

Microbiologists at NYU Langone Medical Center say they have what may be the first strong evidence that the natural presence of viruses in the gut -- or what they call the 'virome' -- plays a health-maintenance and infection-fighting role similar to that of the intestinal bacteria that dwell there and make up the "microbiome."

In a series of experiments in mice that took two years to complete, the NYU Langone team found that infection with the common murine norovirus, or MNV, helped mice repair intestinal tissue damaged by inflammation and helped restore the gut's immune defenses after its microbiome had been wiped out by antibiotic therapy. In a report on their work to be published in the journal Nature online Nov. 19, researchers say they also found that MNV bolstered the immune system in fighting off tissue damage.

"Our research offers compelling data about the mutually supportive relationship between viruses and bacteria in the mouse gut and lays the groundwork for further research on precisely how the virome supports the immune system, which likely applies to humans, as well," says senior study investigator Ken Cadwell, PhD, an assistant professor at NYU Langone.

"We have known for a long time that people get infected all the time with viruses and bacteria, and they don't get sick," says Cadwell. "Now we have scientific evidence that not every viral infection is bad, but may actually be beneficial to health, just as we know that many bacterial infections are good for maintaining health."

According to Cadwell, until now, scientists have had mostly trace genetic evidence of a virome's existence, but none to confirm its normal presence in the gut or to clarify whether it plays a harmful, neutral, or helpful role.

What the NY Times had to say about this new area of research:

Viruses as a Cure

When we talk about viruses, usually we focus on the suffering caused by Ebola, influenza, and the like. But our bodies are home to trillions of viruses, and new research hints that some of them may actually be keeping us healthy.

“Viruses have gotten a bad rap,” said Ken Cadwell, an immunologist at New York University School of Medicine. “They don’t always cause disease.” Dr. Cadwell stumbled by accident onto the first clues about the healing power of viruses. At the time, he was studying the microbiome, the community of 100 trillion microbes living in our bodies. Scientists have long known that the microbiome is important to our health.

Kristine Wylie, a research instructor of pediatrics at Washington University School of Medicine who was not involved in the research, speculated that in real life, certain viruses might be important partners with the microbiome. “It isn’t hard to imagine that the viral exposures we get as children are important to our development,” she said.

Published on

Read the labels on personal care products, and do NOT buy those with triclosan! (See earlier posts for other reasons to avoid triclosan.) From Science Daily:

The 'dirty' side of soap: Triclosan, a common antimicrobial in personal hygiene products, causes liver fibrosis and cancer in mice

Triclosan is an antimicrobial commonly found in soaps, shampoos, toothpastes and many other household items. Despite its widespread use, researchers report potentially serious consequences of long-term exposure to the chemical.The study, published Nov. 17 by Proceedings of the National Academy of Sciences, shows that triclosan causes liver fibrosis and cancer in laboratory mice through molecular mechanisms that are also relevant in humans.

"Triclosan's increasing detection in environmental samples and its increasingly broad use in consumer products may overcome its moderate benefit and present a very real risk of liver toxicity for people, as it does in mice, particularly when combined with other compounds with similar action," said Robert H. Tukey, PhD, professor in the departments of Chemistry and Biochemistry and Pharmacology. 

Tukey, Hammock and their teams, including Mei-Fei Yueh, PhD, found that triclosan disrupted liver integrity and compromised liver function in mouse models. Mice exposed to triclosan for six months (roughly equivalent to 18 human years) were more susceptible to chemical-induced liver tumors. Their tumors were also larger and more frequent than in mice not exposed to triclosan.

The study suggests triclosan may do its damage by interfering with the constitutive androstane receptor, a protein responsible for detoxifying (clearing away) foreign chemicals in the body. To compensate for this stress, liver cells proliferate and turn fibrotic over time. Repeated triclosan exposure and continued liver fibrosis eventually promote tumor formation.

Triclosan is perhaps the most ubiquitous consumer antibacterial. Studies have found traces in 97 percent of breast milk samples from lactating women and in the urine of nearly 75 percent of people tested. Triclosan is also common in the environment: It is one of the seven most frequently detected compounds in streams across the United States.

More about this study plus a discussion about the FDA's lack of action. From The Atlantic:

The Ingredient to Avoid in Soap