Scientist culture critical gut bacteria

Example of a segmented filamentous bacteria.

Scientists from France recently announced in Nature that they had successfully cultured segmented filamentous bacteria (SFBs) for the first time.  These bugs likely exist in the intestines of all mammals, including humans, and research has shown they may be amongst the most important commensal bacteria we have.  Previous research has shown that the existence and abundance of SFBs is directly linked to the induction and recruitment of immunity cells, like T cells.  The SFBs exist right on the mucosal boundary of the gut and appear to intimately interact with it.  This close interaction allows the bacteria to use the gut to survive, but also to send molecular signals to the body.

The scientists were able to culture the bacteria by first culturing epithelial cells (i.e. the cells that line the gut) and then culturing the SFBs in close proximity.  During their experimentation they discovered that the bacteria grew best when they were physically touching the epithelial cells, but that they could survive so long as they were close by.  The scientists also discovered many of the important requirements for successful colonization and growth of SFBs, and we invite anyone interested in learning more to read the article.

While the results of this study may not sound very exciting to the lay-man, they are in fact significant.  If these SFBs turn out to indeed be a critical component to mediating the immune system, being able to culture and perform experiments on them in the lab will be essential.  Future studies could possibly identify the key molecules that are critical in signaling host immunity by the microbiome, and important compounds could be made into therapeutics.

The role of the gut microbiome in Down Syndrome

Down Syndrome is the most common genetic cause of intellectual disability and occurs when there is an extra 21st chromosome, trisomy 21. Down Syndrome patients often experience premature aging and are therefore at early risk for age-related conditions like Alzheimer’s disease. Scientists from Italy published a study in November in PLOS One that compared the gut microbiome of Down Syndrome patients with that of healthy individuals.

The scientists hypothesized that the gut microbiome of Down Syndrome (DS) patients was contributing to the aging of the patients and would present similarly to the microbiome of an aged individual. They compared the gut microbiome of 17 patients with DS with previously published data for 16 age-matched individuals as well as 5 elderly individuals and 3 individuals who were 100 years old.  Interestingly, they found that the microbiomes of patients with DS were very similar to the microbiomes of healthy individuals. In this case, their hypothesis did not end up as they predicted. 

It is important to note that this study only included 17 test subjects who were all under the age of 35.  Future studies will need to be conducted with larger patient cohorts as well as older patients to truly get a good understanding of the gut microbiome profiles of the entire population of patients and better understand this hypothesis. 

There was, however, an unexpected finding that I found to be quite interesting. While the general makeup of the DS patients' microbiomes were similar to those of healthy individuals, there were subpopulations of bacteria that were more or less abundant in DS patients. Individuals with DS had elevated levels of Parasporobacterium and Sutterella and reduced levels of Veilonellaceae. This increase of Sutterella and decrease of Veilonellaceae has previously been described in autistic children with stomach problems. Specifically in this study, Sutterella abundance was positively correlated with Aberrant Behavior Checklist (ABC) scores for the DS individuals. The ABC test is a 58 item report checklist used to assess maladaptive behavior in people with developmental disabilities. 

This positive correlation tells us that this bacterium in the gut may play a role in maladaptive behavior in patients with various conditions. Although the original hypothesis was not confirmed, this very interesting result will need to be further explored to better understand the role of the gut microbiome in individuals with autism spectrum disorder and Down Syndrome.

Could ice cream prevent cavities?

We know that the oral microbiome hosts a wide variety of bacteria, some good, and some that cause cavities.  Those that cause cavities do so by producing acid as they break down the food in our mouths.  Researchers in India are trying to discover if probiotics could help alter the oral microbiome so there is a decrease in the bacteria that commonly cause cavities.  In their study they investigated a type of ice cream sold in India that has the probiotics Bifidobacterium bifidum and Lactobacillus acidophilus mixed in with the ice cream.  The researchers were interested in the effects the probiotic ice cream on the levels of bacteria and fungi in saliva, namely Streptococcus mutans, Lactobacillus acidophilus, and Candida albicans, because these three bacteria are the main causes of tooth decay.  The results were recently published in the Journal of Dental and Medical Sciences.

In the study, the researchers gave 20 participants one dish of ice cream each day for 10 days that either contained the probiotics or did not.  The researchers examined the bacteria in the participants’ saliva both before and after the ice cream intervention.  The results showed that consumption of probiotic ice cream caused a significant reduction of both S. mutans and C. albicans, and an increase in the number of L. acidophilus when compared to controls.  The increase in L. acidophilus is not surprising because the ice cream contained L. acidophilus. The researchers highlighted that in other studies of people eating Lactobacillus acidophilus, it did not persist in the individuals’ mouths.  Overall, two of the cavity causing bacteria decreased in abundance and one, which was in the probiotic ice cream, increased in abundance.

We must admit that the rigor of this study was highly lacking, so we don’t want anyone to take these results too seriously. While more research needs to be done to determine if probiotic ice cream can actually help prevent cavities and tooth decay, any study that recommends eating it is fine by me.  It’s obviously important to brush your teeth every day, but it’s definitely more fun to eat ice cream than to floss!

Probiotics may help fight the flu

The influenza viruses are the devastating viruses that cause the flu.  They highly communicable and can cause pneumonia, ear infections, sinus infections, asthma and even diabetes.  Basically, they are really nasty bugs that people have been suffering from, and trying to get rid of, for at least the last 2000 years.  One possible treatment, which is now being explored, is the use of probiotics to prevent flu and its virulence.  Scientists in Japan recently tested how one type of probiotic, Bifidobacterium longum, could combat the flu in mice.  They published their results in Microbiology and Immunology.

Mice were divided into two groups, one which received the B. longum for 17 consecutive days in their drinking water, and one which did not.  On day 14 of the study all the mice were infected with flu via injection.  The researchers then monitored all of the mice to see the effect of the probiotics.  Surprisingly, the mice which received the probiotics had improved clinical symptoms as compared to those that did not.  For example, the mortality rate dropped from 70% to 35% after 12 days in those mice that had been given probiotics.  In addition, the probiotics seemed to help with breathing and general activity as well as kept mice from losing as much weight as the control mice.  Beyond this, the probiotics appeared to decrease the proliferation of the influenza in the respiratory tract, which resulted in a suppression of overall inflammation as compared to the mice without probiotics.  Finally the researchers presented evidence for several possible pathways by which the probiotics were helping the mice.

This study is fascinating in that it shows a simple, yet powerful tool to alleviate the flu in mice.  It also begs for a follow-up study to see if the same type of probiotic response would be observed in mice infected with rhinoviruses, the cause of the common cold.  While we here at the AMI encourage everyone to get vaccinated for the flu, if for whatever reason you cannot, perhaps consider eating a bit more yogurt this winter.

A high fiber diet combined with the right microbiome may help prevent colon cancer

Colon cancer is the third leading cause of death worldwide. It is caused by a number of genetic changes over time and while it can be hereditary, it is largely based on diet and lifestyle.  The role of fiber in colorectal cancer has been largely debated due to numerous studies with varying results. A recent study in Cancer Discovery provides strong evidence that dietary fiber does in fact protect against colon cancer. 

Scientists took mice that were bred to have no bacteria in their guts, called gnotobiotic mice, and colonized them with Butyrivibrio fibrosolvens, a bacterium that produces butyrate. The mice were then exposed to either a high or low-fiber diet. The mice that were fed a high-fiber diet were protected against colorectal carcinoma.  However, mice exposed to a high fiber diet that were not colonized by B. fibrosolvens were not protected against the carcinoma, telling us that the microbiome of the mouse as well as the high-fiber diet resulted in this protection and not the fiber alone.

Several epidemiological studies over time have failed to show a connection between fiber intake and colon cancer. This study suggests that this may be due to the studies’ failure to control for the study participants’ microbiomes. High fiber alone does not protect against colon cancer but in conjunction with a microbiome that produces high levels of butyrate, they may be protected from colorectal carcinoma.  The authors of this study suggested that past studies should be revisited to look at differences in the microbiomes of participants. It will be interesting to see what findings are made as a result of this discovery and if in fact epidemiological studies are done to control for the microbiome.  

Bacteria may be responsible for chronic prostatitis

Editors note: Two of our blog posts on aging and the microbiome were recently shared with the website Gut Microbiota for Health. Our readers should take a look!

Link to post.

Some people suffer from an enigmatic diagnosis known as urologic chronic pelvic pain syndrome (UCPPS), 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 there 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.”