BioQuakes

AP Biology class blog for discussing current research in Biology

Tag: microbiome (Page 1 of 3)

Your Gut Microbiota Could be Influencing Mental Health Disorders: Could Psychiatric Medications Change This?

Mental Health and Gut Bacteria 

Newly published research in rodents and continuing research in humans explores the effects of psychiatric drugs, including antidepressants, on the composition of gut bacteria. They have examined how the effects on gut microbiota, typically caused by naturally occurring metabolic changes in the gut, may influence connection with the nervous system rendering some negative effects on mental health. The most common mental health conditions connected to changing composition of the gut microbiome are anxiety and depression. 

This comes from a recent study that Medical News Today has released, reporting on different bacteria that play a part in synthesizing neuroactive compounds in the gut. These neuroactive substances interact with the nervous system, influencing the likelihood of developing depression or anxiety. This research has been proved more extensively and directly in rodents, but the research in humans provides similar conclusions, allowing scientists to partially conclude the effects in humans–research on this topic in humans is likely to expand greatly in the near future. 

How can gut microbiota be affected by different psychotropics? 

The Study and Results:  

Provided this link between changing gut bacteria and mental health, researchers from University College Cork, in Ireland, set out to investigate this in rodents. First, the team “investigated the antimicrobial activity of psychotropics against two bacterial strain residents in the human gut, Lactobacillus rhamnosus and Escherichia coli.“The psychotropics that the researchers conducted this study with included fluoxetine, escitalopram, venlafaxine, lithium, valproate, and aripiprazole.

Then, the scientists studied “the impact of chronic treatment with these drugs” on the rats’ microbiota. The scientists gave the rodents psychiatric drugs for a period of 4 weeks, ending the study by inspecting the effects of the drugs on the rodents gut bacteria. They found that lithium and valproate, mood stabilizers that can treat conditions including bipolar disorder, raised the numbers of certain types of bacteria. These included Clostridium, Peptoclostridium. On the other hand, selective serotonin reuptake inhibitors (SSRIs), fluoxetine and escitalopram (both antidepressants), ceased the growth of bacterial strains such as Escherichia coli.

“We found that certain drugs, including the mood stabilizer lithium and the antidepressant fluoxetine, influenced the composition and richness of the gut microbiota,” says head researcher Sofia Cussotto. 

Conclusions from the Study, and what the Future Holds 

Dr. Serguei Fetissov, a professor of physiology at Rouen University, in France commented on the study, saying: “At the moment, it would be premature to ascribe a direct role of gut bacteria in the action of antidepressant drugs until this work can be reproduced in humans, which is what the authors now hope to do.”

However, the implications and further goals and hopes of this research is to directly prove that “psychotropic drugs might work on intestinal microbes as part of their mechanisms of action,” says Cussotto

Do you think it is too early to assume a direct connection between gut bacteria and mental health in humans? Comment about this below.

Further Research

https://www.medicalnewstoday.com/articles/amp/326299 

https://www.medicalnewstoday.com/articles/319117.php#1 

 

 

 

How our day-to-day food intake shapes our gut microbiota

Our diet is a significant modulator of changes in our gut microbiota structure, particularly at an individual level. The concept that what we eat is related to health is not a new idea. With new studies and experiments on the human gut microbiota, scientists are finally beginning to truly understand how exactly food impacts our health. The commonly heard phrase “you are what you eat” has been proven true. If you were to et a strawberry or hamburger, the food enters your digestive system and comes across the intestinal microbes. The way your body processes the food is influenced by the microbes that are living in your gut.

This is an image of food items that would help to create a balanced healthy diet.

Other than only being related to diet, levels of physical activity and sleep patterns can also affect the human gut microbiota. In a recent study, “for 17 consecutive days, 34 healthy participants were asked to self-record their food consumption using a food report.” From the results, the researches concluded that the variation in the daily microbiome is related to food choices, and not to standard nutrients.

For example, a vegetable such as spinach, which is rich in iron and also contains many other nutrients, such as fiber, minerals, and carbohydrates. All of these nutrients help to strengthen spinach’s relationship with the gut microbiome. Therefore, “nutritional advice should focus more on recommending people combine fruit and vegetables in their daily diet instead of prioritizing specific fibers.”

To conclude, a varied diet helps to maintain a well-balanced microbiome while also at the same time also giving your body the nutrients it needs in order to stay healthy.

How can we survive on raw foods out in the wild? Microbes may help.

In a recent study, Vayu Maini Rekdal was ordered to create a menu with foods that could be eaten either cooked or raw. He made chia seed breakfast puddings for volunteers who would eat the food cooked or eat the food raw. Their stool samples would then be taken so that Professor Rachel Carmody could analyze the microbes that had a role in the digestion in the different styles of food. She had previously found out that the microbiomes within mice quickly changed when they went from raw sweet potatoes to cooked sweet potatoes and she wanted to see if that rang true in humans as well.

The results of her human experiment showed that the microbiomes within the human gut changed rapidly like that of the mice once the diet was changed. However, she found that the microbiomes didn’t change drastically between raw and cooked meat, unlike the sweet potatoes. Dr. Carmody explained that it is necessary for the microbiomes to shift when eating raw sweet potatoes because it is harder for humans to digest them when they are raw and cooking them changes the types of molecules that need to be digested.

Dr. Carmody believes that the microbiomes are able to change so quickly because our ancestors might have needed to change diets quickly when they didn’t have access to a certain type of food. Even though we could be eating food that is uncooked, less tasty, and harder to eat, our gut microbes allow us to adapt to those types of food in order to stay alive. Therefore, it could be thought that our microbiomes have evolved alongside humans. However, she also found that mice are able to survive on the microbes that are found within humans, which leads some to believe that humans haven’t totally co-evolved with our microbiomes.

More research must be conducted in order to get a better understanding on the interactions between humans and their microbiomes since it is a very complex relationship. Why do you think it is important to learn more about our microbiomes? Maybe one day we can start eating foods that were previously unable to be eaten.

 

 

Discovering and Using Your Personal, Biological, Tiny Army

Bacteria is an important part of our biology, so important that we are essentially 99% bacteria. A lot of this bacteria is part of the human gut microbiome. This topic has been picking up interest in the field of biology, and have shown linkage to many diseases such as inflammatory bowel disease and obesity. Not only do the bacteria in our gut play a role in preventing these diseases, but their symbiotic relationship helps us maintain metabolic functions.

File:The first and second phases of the NIH Human Microbiome Project.png

This is a depiction of the numerous types of bacteria in our microbiome.

Until recently we were unable to study these bacteria due to our inability to cultivate them in a lab; however, due to new advancements in sequencing technology we can now see how big of  role they play in our biology and our functions. These bacteria are “estimated to harbor 50- to 100-fold more genes, compared to the hose. These extra genes have added various type of enzymatic proteins which were non-encoded by the host, and play a critical role in facilitating host metabolism.” For example, gut microbiata is very important in fermenting unabsorbed starches. These bacteria also aid in the production of ATP. A certain type of bacteria generates about 70% of ATP for the colon with a substance called butyrate as the fuel.

File:Immune Response to Exotoxins.png

This image shows the interaction between the gut and the immune system. The immune system targets bacteria, but somehow not our gut bacteria. 

Another large role of the gut microbiome is its interactions with out immune system and nervous system. The bacteria in our gut suppress the inflammatory response in order to not be targeted by the immune system. This allows for a symbiotic relationship between us and the bacteria inside of us. This allows the gut bacteria to help regulate the inflammatory response without being stopped by the very thing it’s regulating. Without these bacteria our inflammatory responses would be completely out of the ordinary.

These findings with gut bacteria are fairly new and there is much more to come regarding their use in the field of medicine. Something to think about that I found fun was how little of us is really human. Ninety nine percent of you is bacteria, which essentially means that we are pretty much just giant colonies of bacteria. Kind of gross/amazing when you think about it.

Is it Time For a Raw Food Diet?

A recent article details a study by scientists at UC San Francisco details the effects of cooked food versus raw food on the gut microbiomes of mice. By feeding some mice raw potato and others cooked potato, scientists discovered that in mice, raw food damages certain microbes. Scientists discovered that raw foods contain antimicrobial compounds that damaged microbes in mice. Surprisingly, differences between the mice were due to chemicals found in plants. Turnbaugh’s is currently analyzing the specific chemical changes that occur after cooking in order to further understand how cooked food impacts the mice microbiomes.

 

Another interesting effect of the raw food on mice was weight loss. The researchers were curious as to whether the weight loss was due to the altered microbiomes. They were ultimately not due to the microbiomes, because when the altered microbiomes were put into mice eating a normal diet, those mice put on fat. The researchers are currently unsure of why this happens.

Interested in the possible ramifications of his discovery on human diets, Turnbaugh  conducted a second experiment using human test subjects. The raw food diets altered the microbiomes of the human test subjects, an exciting find for the researchers. The effects of these altered microbiomes are still unclear and is being further researched. For now, raw food diets don’t seem to have massive benefits and in cases of contaminated meat can be harmful to humans, but only further research will tell.

The Making of the Largest Human Microbiome Database

Scientists from all over the world, including China, Denmark and Sweden are planning to design a microbiome map of the human body. These scientists will be be analyzing over one million microbial samples from the mouth, skin, reproductive tract and the intestines to complete their goal. This article states that in order to provide a baseline of micro ecology research on a very large population sample, the scientists will explore and use Mouse Genome Informatics to draw their map.

 

Dr. Liu Ruixin from the Shanghai National Clinical Research says, “By studying the changes in the human microbiome between the normal and pathological states, before and after treatment in larger metagenomics datasets, and analyzing its effects on human metabolism and health, in the future we will provide more possibilities for new therapies in many fields such as metabolic diseases, cancer, reproductive health and newborn health.”

So far, scientists have analyzed over 10,000 samples of metagenomic sequencings.

This research will be important for future studies, projects and treatments because it will provide context and specific information about the human microbiome.

 

This photo captures the structure of DNA that will aid the scientists in developing the map.

Should We Be Carbo-loading? The Effects of Resistant Starches on the Gut Microbiome.

What is Starch?

By definition starch is a polysaccharide composed of a chain of glucose molecules held together by glycosidic bonds. Starch is common in nearly all green plants and is used for short term energy storage.

Different Types of Starches

Starch can come in two distinct forms: amylopectin a compound with a complex system of branching glucoses, and amylose a simple straight chain of glucose molecules. Because of amylopectin’s larger and more complicated nature it has a much larger surface area than amylose making it significantly easier to digest. The amylose cannot effectively be broken down by the enzymes of the digestive system. Instead it is left to be dealt with by the human gut microbiome. For this reason it is commonly referred to as a resistant starch.

How are Resistant Starches Beneficial?

An international research article including authors from Harvard Medical School suggests that resistant starches have a myriad of benefits. Some resistant starches which thwart digestion in the stomach and small intestine, make their way all the way down to the large intestine where they are subject to fermentation by the microscopic bacteria of the human gut. The fermentation process can metabolize a multitude of different useful products. For example some significant and common place output of gut fermentation are simple fatty acids. One key short chain fatty acid created during this process is Butyrate, the preferred fuel oof the cells lining the colon. In addition to Butyrate there exist many other short chain fatty acids that help maintain and fuel the body. These fatty acids can be used for many different purposes, all beneficial to both the gut microbiome and the host. The benefits may range from weight loss to curbing the progression of chronic kidney disease.

In addition to their ability to be changed into more useful forms, resistant starches also serve to enhance the effectiveness of the gut microbiome. Constant ingestion of resistant starches can stimulate an increase in the size and health of gut microbiomes in addition to raising host metabolism.

Common Uses For Resistant Starches

Resistant starches are often used in weight reducing diets in order to encourage an increase in metabolic rates. Although results of these diets are often compelling, a diet must consist of all types of food groups and should contain a variety of vitamins and minerals. Eating only amylose and other resistant polysaccharides will not on its own help you achieve weight loss. It should be paired with exercise and an otherwise healthy diet.

Should resistant starches be used in dieting or do they promote malnutrition? There are many benefits to a diet high in resistant starches, including building up a healthy gut microbiome. However you cannot survive solely on carbohydrates. This is a complex question, and I would be interested in hearing your opinions in the comments.

 

 

 

Secure Passcodes : Not Just For Your Computer… But For Your Gut

What is the Human Gut Microbiome?

Human gut microbiomes are made up of all the bacteria present in your gut. The Bacteria in your gut outnumbers the cells by a ratio of 10 to 1. While the presence of that much bacteria sounds like a bad thing, it can be confirmed that “the gut microbiome is very important for human health—that much we certainly know”.  The nearly 100 billion Bacteria cells per gram are actually what helps the body digest food and remove the bacteria that is bad for your gut.

 

(Left) Bacteria on vs not on the intestines       (Right) Gut Microbiome Graphic

A Unique Passcode

As said above, the human gut microbiome is essential to digesting food but more importantly keeping our body healthy. The thought of controlling a person’s gut bacteria in order to keep them healthy and fight illness is fascinating to scientists. The key to using the microbiome to fight sickness is in the “passcode” that is essential to unlocking its potential. Each microbe, according to recent research, requires a unique passcode. The research done by scientists according to phys.org says that once there is a way to determine the “passcode” it will unlock a whole new world of probiotic treatment in the future.

Why Else is the Microbiome important

According to other research done within the past few years, it has been found that sleep can also be linked to the human gut and stomach. The quality of sleep a person gets can be linked to their “biological rhythms, immune function, and nutrient metabolism” however it is still unknown to what extent the microbiome is affecting human sleep.

Conclusion

While researchers still have many questions about the human gut microbiome and how it contributes to health, wellness, and overall human biology, once they have come to some more concrete conclusions the impacts of controlling the bacteria in the human gut would exponentially improve the health of many people. It may sound weird that your bacteria have a “passcode” with which to be controlled, but hey, conclusive findings of the microbiome could even help you get a better night’s sleep! And who doesn’t want that?

Can your diet’s effect on gut bacteria play a role in reducing Alzheimer’s risk?

Could following a certain type of diet affect the gut microbiome in ways that decrease the risk of Alzheimer’s disease? According to researchers at Wake Forest School of Medicine, that is a possibility.

In a small study, researchers were able to identify several distinct gut microbiome signatures in study participants with mild cognitive impairment (MCI), but not in the other participants with normal cognition. Researchers found that these bacterial signatures correlated with higher levels of markers of Alzheimer’s disease in the cerebrospinal fluid of the participants with MCI. Additionally, through cross-group dietary intervention, the study also revealed that a modified Mediterranean-ketogenic diet resulted in changes in the gut microbiome and its metabolites that correlated with reduced levels of Alzheimer’s markers in the members of both study groups.

“The relationship of the gut microbiome and diet to neurodegenerative diseases has recently received considerable attention, and this study suggests that Alzheimer’s disease is associated with specific changes in gut bacteria and that a type of ketogenic Mediterranean diet can affect the microbiome in ways that could impact the development of dementia,” said Hariom Yadav, Ph.D., assistant professor of molecular medicine at Wake Forest School of Medicine.

The randomized, double-blind, single-site study involved 17 older adults, 11 diagnosed with MCI and six with normal cognition. These participants were randomly assigned to follow either the low-carbohydrate modified Mediterranean-ketogenic diet or a low-fat, higher carbohydrate diet for six weeks then, after a six week “washout” period, to switch to the other diet. Gut microbiome, fecal short chain fatty acids, and markers of Alzheimer’s in the cerebrospinal fluid were measured before and after each dieting period.

The limitations of the study included the subject’s group size, which also accountns for the lack of diversity in terms of gender, ethnicity, and age.

“Our findings provide important information that future interventional and clinical studies can be based on,” Yadav said. “Determining the specific role these gut microbiome signatures have in the progression of Alzheimer’s disease could lead to novel nutritional and therapeutic approaches that would be effective against the disease.”

Each human contains trillions of organisms that influence our metabolism, immune function, weight, and even cognitive health. It is so fascinating to examine the role of gut microbiomes in the progression of Alzheimer’s disease. I believe diets can be very controversial, and I find it interesting to see researchers in this study show how the Mediterranean-ketogenic diet may be effective against Alzheimer’s. However, I am so intrigued to see where these findings may take us with approaches that may be effective against Alzheimer’s, whether they be nutritional or therapeutic approaches.

Virus VP882: Our Forgotten Spy to End our Bacteria Problem

The virus VP882, which had long ago sequenced in Taiwan as a part of a study of an outbreak of cholera, has now resurfaced and has the potential to make major waves in our addressing of the harmful bacteria. In recent years, biomagnification of harmful bacteria, in large part due to human waste, like Escherichia Coli and Vibrio Cholerae are having immediate and detrimental effects on our environment and in human health as well. For example, a significant amount of produce circulating in the United States has been contaminated with Escherichia Coli causing many to contract Shiga toxin-prducing E. coli infection (STEC) which, as according to the Centers for Diseases Control and Prevention (CDC), can causes “severe stomach cramps, diarrhea (often bloody), and vomiting”.

Our problem today is that the production of bacteria-specific responses to infection are difficult to produce and become costly as a result. Most of our anti-bacterials today target bacteria-made toxins, in order to restore affected G-Protein cell signaling function. Unfortunately, this treatment may negatively impact the integral human microbiome. An alternative way of countering bacterial infections is through use of phage therapy. This treatment is much more specific, bringing less harm to the host organism, and involves viruses to enter and reproduce in bacterial cells, eventually causing them to lyse, thus killing them. While objectively this process seems far superior than the current general treatment, too often the infective bacteria remains unknown, which as M.I.T. Professor Mark Mimee discusses in the Scientific American article on the VP882 virus, forces doctors to prescribe “a cocktails of different phages. But manufacturing cocktails and adhering to drug regulations is too expensive.” Then enters the VP882 virus.

The VP882 virus works just as most other bacteriophages: the virus uses bacteria as hosts for their reproduction, and cause them bacteria cells to lyse, after they have hijacked a given bacterium’s reproductive mechanisms. There are two things, though which make this virus special in the realm of bacteriophages. VP882 has the ability to sense bacterial cell communication and is a very simple structure, similar to a plasmid. This virus’s discovery can in part be credited to a coincidence. A student at Princeton, Justin Silpe, in his study of a molecule, DPO, which is integral in bacteria cell signaling, specifically quorum sensing, ran across this surprising virus which was sequenced in the presence of DPO. What he and his professor, Bonnie Bassler, found is that this virus, which was attacking cholera cells, was able to secretly calculate the optimal time to invade the bacteria (thus its many comparisons to a spy), by sensing a high quantity of DPO, which is a signal for when bacteria can begin their collective behavior, and possibly start a disease. What this means is that because of this ability to understand a bacteria’s quorum, they can most effectively counteract an infection.

In addition, upon further study, VP882 was found to be a very simple structure. This arguably the most important aspect of VP882. The virus is very similar to a plasmid, which can be easily modified and, thus accepted by a plethora of bacteria. This leads scientists like Bassler and Silpe to believe that VP882 can be modified to create an all-encompassing bacteriophage treatment, one which could be made cheaply and work far more effectively than general anti-bacterial treatments. Whether this is feasible still remains unknown, but in the time being, VP882 can be readily applied to neutralizing cholera in industrial wastewater without harming the natural microbiome, proving already the usefulness of this discovery.

https://commons.wikimedia.org/wiki/File:Discharge_pipe.jpg

Discharge Tube Releasing Cholera-filled Wastewater

 

 

I Have a Gut Feeling that Microbiomes Are the Next Step in Medicine

We as humans are a very genetically diverse species. But what if we could find microorganisms that have over 150 times more genes right within our own guts. Scientists believe that human microbiomes is the key to treating diseases in the future and some analysts believe that the field of human microbiome market will reach $3.2 billion by 2024.

Lack of microbiome diversity has shown to cause diseases like MS, diabetes, and asthma. So microbiomes have demonstrated themselves to be a key component of our health. To better understand these links, many projects launched in the past few years have focused on mapping microbial genesthat are associated with disease. For example, there are certain microbiomes that make cancer drugs ineffective whereas others are actually necessary to make these drugs work. Thus, a patient’s microbiome makeup directly correlates to their survival chances. So the next step in the Microbiome market is modifying the microbiome to work for the patient.

One older technique of doing this is traced back to China thousands of years ago where they would transplant whole microbial communities to treat diarrhea also known as Fecal microbiota transplant (FMT). A more defined approach is where beneficial bacterial strains are delivered, alive, to the patient’s gut.

In the UK, a company called Microbiotica transfers non-pathogenic strains of C. difficile to fight C. difficileinfections, IBD, and cancer. Even though these approaches have drawn a lot of attention to the field, some scientists argue that the bacteria we ingest are not as well adapted to living in our gut as those that have been living there for years thus are not effective.

In France, an opposite approach is used by Enterome where drugs target specific bacteria leaving the rest to the gut microbiome intact. This approach is aimed at treating Chron’s diseaseand cancer.

Another approach is using bacteriophages to kill specific bacteria strains. Eligo Bioscience takes it a step further by using the bacteriophages to deliver CRISPR/Cas9 into the bacteria to kill it by cutting the DNA of the strain carrying the disease only.

Finally, certain companies like Blue Turtle Bio engineer bacteria to make them produce drugs directly within the human gut.

Since this is a rather new field, there are newly emerging companies along with groups who do not believe in the practice. Personally, I do believe in this practice because there is already a strong correlation between our immune system and specific microbiome strands. With microbiome treatments comes microbiome diagnostics to determine which patients can benefit from these therapies. Thus a high number of approaches will initially fail to treat disease. So far, gut infections and inflammatory diseases seem to be strongly correlated to the gut microbiota, so that will be an area where more research should be applied.  A crucial challenge for the field will be to move from correlation to causation, and a lot of research is still needed for that.

 

An Exception to Microbiome Functionality

A recent study was developed to understand how HIV corresponds to the microbial communities of the female sex organ. Dr. David Fredericks- a physician and college professor that teaches “Allergy and Infectious Disease” at University of Washington, led a study on the relationship between the diversity of bacteria in the vagina and how it may lead to HIV. The research population specifically focused in on sub-Saharan African women, who make up 56% of the continent’s infected population.

HIV-infected T cell

Scientists have come to discover that the greater the diversity of a microbiome, the more equipped that region of the body is for combating infections. Although- this concept is strictly relative to the mouth, intestines, and nasal passageway because a variety of bacteria inhabiting a vaginal microbiome can be very detrimental to a woman’s health. One of the leading risks from having a diverse vaginal microbiome community is the “human immunodeficiency virus”.  This virus can be transmitted through sexual contact, childbirth, nursing, or the usage of unsanitary needles. One’s immune system is weakened after contracting HIV because CD4 cells are damaged, which makes it harder for the body to fight off illness. Dr. Fredericks has revealed that the presence of a microbe called Parvimonas Type 1 is usually not a dangerous bacteria, yet the microbe is linked to the virus when there is a higher concentration of it in the vaginal microbiome.

Dr. Fredericks accomplished making this new find by using a strategy called the “dose-dependent effect” to measure the amount of “bugs” in a microbiome community in correlation to the risk of contracting HIV. In doing so, the scientists took cultures from 87 women who were infected with HIV and 262 cultures from women who tested negative for HIV to compare the bacterias found in both microbiomes. During the second half of the study, biologists used screening through a method called “PCR“and identified 20 types of bacteria that could potentially be linked to the virus. The bacterias involved in generating the virus in the female reproductive system were narrowed down to seven specific strains of rogue bacteria. Since the discovery, the biggest question revolving around HIV is determining how to permanently reduce the concentration of these illness-inducing bacterias.

The Microbiome of the African Hunter-Gatherer

Photo Credit: Andy Lederer on Flickr

In a study published on August 24th, 2017 on the gut microbiomes of the Hadza people of Tanzania, several key findings were brought forth on how our microbiomes work.  The microbiome is the trillions of bacteria cells that live in and on all multicellular organisms.  Our knowledge on microbiomes is somewhat limited, but that didn’t stop this team of scientists, led by Justin Sonnenburg of Stanford University, who aimed to track the differences between the microbiomes of different peoples and to catalogue the vast array of bacteria that the microbiome is comprised of.

The Hadza, as a hunter-gatherer group, vary their diet heavily depending on the Tanzanian seasons.  During the dry season, they have more access to hunted game. During the wet season, their diet is mainly comprised of berries and honey.  The bacteria present in their microbiomes when tested during the different seasons reflects this change in diet.  Microbes such as the phylum Bacteriodetes varies heavily with the seasons, a trend which has been seen in several other nonindustrialized groups.

The researches then compared their findings among the Hadza to industrialized peoples as well as other nonindustrialized peoples and found that “the groups of microbes that varied seasonally in the Hadza were largely absent in the industrialized microbiomes, but present in the microbiomes of people who live similarly to them.”  This is further evidence on the relationship between the human microbiome and environment that could play a key role in the future as we discover how the microbiome affects human health.

For the original article on this study, click here

This Easy Method Will Make Sure You Never Get Strep Again

More than 3 million people a year get diagnosed with strep throat, however since it is a minor illness that is very easily treated, people do not see the issue with getting sick almost every year. Because bacteria reproduce in just a few days, many generations of bacteria go by very quickly; and every time they reproduce, they are also evolve.  Meaning, every time one takes antibiotics, the bacteria becomes more and more resistant to it, until we can’t kill them anymore with the same antibiotic.

For many humans around the world, the thought of not being able to fix a simple bacterial infection with an antibiotic is quite frightening; however recent discoveries about the human microbiome puts this fear away.

Bacteria at the microscopic level

There are many helpful bacteria that live in the throat and mouth. Most of these helpful bacteria are probiotics.  The probiotic that specifically attacks strep, is actually another strain of strep called Streptococcus salivarius K12. This probiotic produces two lantibiotics that attack Streptococcus pyogenes, the species that are responsible for the known strep throat.

From this knowledge, scientists did an experiment that gave one group a tablet that, when chewed, released billions of colonies of S. salivarius K12 and gave another group a tablet that did nothing. The group that received the probiotic, showed a 90% reduction in strep episodes than the group that received nothing. This information also helped decrease the time on antibiotics for strep by 30 times.

You can buy doses of S. salivarius K12 here if you are interested in not only staying away from strep throat, but also improving your overall oral microbiome.

If you are interested in reading more about not just the mouth and oral human microbiome, but the whole entire human microbiome; click here!

 

Valuable Poop

Yep, that’s right. Poop can be valuable.

Wait? Isn’t that an oxymoron? Valuable poop?

Yes, as much of an oxymoron as it sounds, poop can be valuable. In a more recent treatment, fecal transplants have proved to be successful in helping with C. difficile infections. Antibiotics stop working, and all hope seems lost. However, there is a solution. Healthy people donate their stool (in the vernacular: poop) to those afflicted by a C. difficile infection in order to restore the health of their gut microbiome. The healthy microbial environment in the healthy stool restores the balance.

Look at that C. difficile, bad stuff!

How does this work? Do the microbiomes go to war?

Truth is, researchers are still trying to figure out exactly how the healthy gut microbiome is restored. We know that C. difficile can take over after treatment with antibiotics because it is faster growing and more resistant to antibiotics. They dominate the other microbes. The insertion of healthy stool with a balanced microbiome into a microbiome that is dominated by C. difficile will restore the microbiome’s diversity and balance. Basically, the healthy gut microbiome will kill or just outnumber the C. difficile, and then the problem is resolved. Scientists still aren´t really sure how this happens but are looking into it.

So what? I’ve never heard of a C. Difficile infection?

Good for you. C. Difficile has actually been afflicting many people in different ways, and some doctors even call it an ‘epidemic’. Even so, this new development has lead researches to believe that this could lead to something bigger. Some have tested if this same technique will help inflammatory bowel disease, to which they had promising results (however, still heterogeneous and statistically inconclusive). This is a creative way of using the microbial environment to help diseases, and an even more creative way to study microbial interactions.

 

Would you get a fecal transplant if it were recommended?

How do you think the C. Difficile is banished by the other microbes?

What do you think regarding the future of antibiotics?

Genetically engineering the microbiome

Researchers from Harvard University have successfully taken the first steps in creating a synthetic microbiome. Using signaling between Salmonella Typhimurium and E. coli, the team was able to promote a new “genetic signal-transmission system” in mice.

A cluster of E. coli, a common species of gut bacteria.

With the hope of inducing interspecies bacterial communication, the researchers manipulated the bacterial signaling method of quorum sensing where bacteria receive and send signaling molecules in order to gauge their population density, performing a group behavior after reaching a certain threshold. By using the variant acyl-HSL quorum sensing, a version absent in mammals, the researchers were able to assess the feasibility of using a signaling system nonnative to its host.

In order to see if the two bacterial species successfully communicated, the researchers introduced both a signaler circuit and a responder circuit into the mice. The signaler circuit, put into Salmonella Typhimurium, contained a gene called luxI that, when turned on by a molecule called ATC, produced a quorum signaling molecule. This molecule was received by the bacteria with the responder circuit, E. coli, triggering a cro gene. This gene then turned on a LacZ gene, which caused the bacteria to turn blue when plated with special agar, and another cro gene, creating a loop that continuously activated the LacZ gene. This served as an indicator, as a blue glow would illustrate if the interspecies communication and the E.coli’s “memory” of it were successful.

After the mice were given the two edited strains of bacteria and placed in a container with ATC-infused water for two days, the researchers analyzed their fecal samples. They found that all of them turned blue, indicating that the genetically engineered signaling system was successful: the E. coli received and remembered a signal from Salmonella Typhimurium in response to an environmental factor. This effective engineered communication, as the Director of Harvard’s Wyss Institute for Biologically Inspired Engineering puts it, is a major step forward in “engineer[ing] intestinal microbes for the better while appreciating that they function as part of a complex community”.

With the basic principles of a synthetic microbiome a success, the researchers now want to experiment with new bacterial species and signaling molecules, bringing them closer towards their ultimate goal of engineering a gut microbiome that can perform tasks ranging from improving digestion to curing diseases. As the “next frontier in medicine [and] wellness,” the microbiome will no doubt be a key pillar of medicinal research for decades to come.

Microbiomes… an Athlete’s Key to Success!

For years, scientists have been trying to see what makes a professional athlete different from someone who didn’t quite make the cut. Is there something that professional and elite athletes have that other athletes or inactive individuals don’t? Is it possible to give a mediocre athlete a supplement to improve their performance? Dr. Jonathan Schieman and George Church from the Wyss Institute at Harvard University believe the answer is yes, and they think they’ve found the answer, microbiomes.

Dr. Schieman and his team conducted thorough research on NBA players, marathoners, and Olympic rowers to see if there was a common microbiome that these high-level athletes all shared that sedentary individuals did not. After immense amounts of testing and making sure the proper controls were in place to avoid confounding, and lurking variables, Schieman and his team were able to find one particular organism that was elevated in the guts of athletes’ bodies more than sedentary individuals.

Schieman and his team were able to isolate a particularly abundant organism in athletes that feeds off lactic acid. Lactic acid is a naturally occurring chemical compound that generates during particularly intense and strenuous muscle exercise. Thus, the researchers believe that the organism they isolated has a particularly important effect on making athletes stronger. In addition, the researchers have recently conducted a new study on rugby players and found that rugby players have more of this organism in their body as well as a more diverse range of microbiomes than a sedentary individual.

The microbiome space is particularly new, so one cannot conclude that these findings will be significant to athletes in the future, a realization that Schieman has come to terms with. However, if Schieman and Church find more conclusive and concrete evidence that these, and other, organisms can yield a much better athlete, the sports world could change forever.

What do you think? Can microbiomes be used to make more elite athletes? Only time will tell.

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The research is from Jonathan Schieman and George Church from the Wyss Institute at Harvard University. A comprehensive scientific journal entry has not been released to the public due to intellectual property concerns, as the findings are part of a privately-owned company.

Image: https://commons.wikimedia.org/wiki/File:EscherichiaColi_NIAID.jpg

Microbiome Genes have Macro-significance

Ever been told that the little things matter in life? This same proclamation that you’ve been told by your elders rings true in your gut: one small modification to your human gut microbiome (a batch of bacteria that call your digestive tract home) can have drastic effects on your metabolism.

A. Sloan Devlin, assistant professor at Harvard medical school, carried out a study that proved the importance of the gut microbiome. She first located the gene in “an abundant gut bacterium” for an enzyme that processes bile acids. She then removed that gene from the bacterium. Next, she “colonized” “germ-free” mice with one of two types of the gut bacterium: either with the bile-processing enzyme or without the bile-processing enzyme. The results were surprising.

Credit: mcmurryjulie on pixabay

After both mice were fed the same high-fat, high-sugar diet, the mice without the bile-processing enzyme “had more fat in the liver and gained weight much more slowly than the other group. They also used proportionately less fat and more carbohydrate for energy.” Changing one single enzyme in a gut bacterium appears to change “whether the host is using [primarily] fats versus carbohydrates” for energy.

Even more staggering was the “correlation of lean body mass to energy expenditure.” Typically, in humans and mice, the more lean body mass an organism has, the more energy it expends. However, for the mice without the bile-processing enzyme, this relationship “broke down.” Devlin hypothesizes that this change could be due to a “signaling,” a process in which “physical states in the body trigger a cascade of genes to switch on or off.” Researchers can use this knowledge to treat diseases: figure out which microbiome bacteria activate which genetic switches, and better treatment for genetic problems such as, acid imbalances, metabolic disorders and obesity, may become a reality.

Devlin is sure to stress that this groundbreaking microbiome research is just her “first step.” Although this study was carried out on “germ-free” mice, Devlin dreams that one day she may use her research to improve the health of her own species: as Devlin states, her research brings her “one step closer to humans.”

 

Genetic Engineering will Create Super Humans?!

“Synthetic microbiome? Genetic engineering allows different species of bacteria to communicate”

Before seeking to analyze how genetic engineering enables the alteration of the microbiome, it is essential to understand the nature of the microbiome. Humans’ microbiomes consist of “trillions of microorganisms (also called microbiota or microbes) of thousands of different species.” Initially, peoples’ microbiomes are solely determined by their DNA; however, as time goes on, a person’s microbiome can be shaped by other factors, including the environment in which they live, or their diet. The microbiome contains both helpful and deleterious microbes, but “In a healthy body, pathogenic and symbiotic microbiata coexist without problem.”

According to researchers from the Wyss Institute at Harvard University, Harvard Medical School (HMS), and Brigham and Women’s Hospital, it may now be possible to create a “synthetic microbiome.” The team did a study in which they utilized a particular type of quorum sensing known as acyl-homoserine lactone sensing. Quorum sensing allows bacteria to regulate the expression of genes and to detect the size of bacterial colonies, through signal molecules. First, the team inserted “two new genetic circuits into different colonies of a strain of E. coli bacteria.” One of the circuits acted as a “signaler” and the other acted as a “responder.”

File:E. coli Bacteria (16578744517).jpg Picture of E. Coli bacteria

In short, the team inserted a single copy of luxl, a gene activated by the molecule anhydrotetracycline (ATC), into the signaling circuit. The signaling molecule formed by this gene then binded to the receptor circuit, which activated another gene, known as cro. The cro gene creates Cro proteins, and these proteins triggered a “memory element” within the responder circuit, in which two more genes, LacZ and another cro, were produced. If the signaling molecule is received (which it was), the presence of LacZ causes the bacterium to turn blue. Most importantly, the additional cro gene essentially keeps the “memory element” on, so this cycle continues.

To make sure that this system works in living organisms, the researchers tested it in mice. Signs of signal transmission in the mouse’s gut between the signaler S. Typhimurium bacteria and E. coli responder bacteria were detected. In other words, the engineered circuits allowed the bacteria to communicate with one another.

While these findings are extremely exciting, scientists have yet to discover whether or not other genetically engineered species of bacteria will also be able to facilitate communication between molecules. A Founding Core Faculty member of the Wyss Institute said that “[They] aim to create a synthetic microbiome with completely or mostly engineered bacteria species in our gut, each of which has a specialized function.” If this is achieved, we will move one step closer to becoming super humans!

Feature Image: “Free for Commercial Use” and “No attribution required”

Whole-Grain Bread: The Healthy Choice…or is it?

Contrary to popular belief, whole-grain bread might not be healthier for everyone. A new study has determined that whether white bread or whole-grain bread is healthier for you depends on the microbes in your gut. After studying 20 people for one week each, researchers found that some people’s blood sugar levels raised after eating standard white bread while others did not. Similarly, they found that some people’s blood sugar rose when eating standard whole grain bread. The researchers, Eran Elinav and Eran Segal, studied the mix of microbes in the stool samples as well as their genetic makeup.

This study is part of a growing group of studies that support personalized nutrition that is customized to your genetic makeup rather than a plan for everyone. The same group has also done other research in the nutrition field in Israel, where they studied how people respond to eating certain foods.

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