BioQuakes

AP Biology class blog for discussing current research in Biology

Tag: gut microbiome (Page 1 of 2)

Running on Bacteria

In a recent article it was found that elite athletes could have a step above average people due to some of the bacteria found in their gut. Researchers took stool samples what from elite runners from the Boston marathon in 2015 and found that there was a spike in appearance of the Veillonella. An in depth definition of what Veillonella is can be found here. For the purposes of the research it was said that these bacteria appears to take lactate produced by the muscles in the body and turns it into a compound that helps out the endurance of a runner. This same trend of increase of Veillonella was also found in 87 ultramarathon runners and Olympic rowers after a workout.

To prove their findings they cultivated one strand of Veillonella called Veillonella atypical from the runners and fed it to mice. They also gave the mice lactate in order to give the Veillonella food to feed on in the mice’s gut. The results to this was a 13 percent increase to the length of time these mice could run. However at the same time not all of the 32 mice that they gave this strand of Veillonella actually reacted to it. With the mice the Veillonella used the carbon from the lactate to grow and ended up producing propionate. An in depth definition of propionate can be found here. Propionate ended up raising the heart rate and oxygen use in the mice. For humans propionate also raises metabolism.

 

The overall take from these experiments give an interesting take on how these elite runners can do what they do. The food that someone eats isn’t the only thing that affects the microbiome in a humans gut. These bacteria could appear in the gut after only one session of working out or it could be something only certain people have and others don’t. It could also just be something that people who don’t focus heavily on running experience but it isn’t quite known yet. These things could also appear to The overall fact that bacteria in the stomach could be a big part of someone being athletically gifted is new and interesting to the scene of science. I find this cool as I’m a runner and a basketball player myself so to see that the bacteria in my stomach is what helps me do everything I do is incredibly interesting. Next time you run a mile or finish a game of your preferred sport thank your gut. The bacteria in there could just be the reason your body can do it at all.

 

Man’s Gut Bacteria Causes Him to Become Drunk Without Alcohol?!

Over a span of six years, a 46 year old man experienced chronic states of drunkenness, but how can that be?

It turns out that he had auto-brewery-syndrome, or ABS. ABS causes carbohydrates in the digestive tract to turn into intoxicating alcohol! Essentially, it is gut bacteria fermentation.  Within auto-brewery syndrome, bacteria is fermented within the gastrointestinal system, producing dangerous amounts of ethanol in the blood.  It is believed that an antibiotic he was prescribed back in 2011 altered his natural gut microbiome, wreaking havoc and causing a multitude of symptoms including “brain fog.”

After traveling to a clinic in Ohio, doctors discovered strains of Saccharomyces boulardii and Saccharomyces cerevisiae, two bacterias known as “brewer’s yeast” for their fermenting and intoxicating qualities. As a result, doctors put him on an anti-fungal and no-carb diet, but with little to no avail he continued to experience flare ups and a fatal blood alcohol concentration of .4%! Doctors at Richmond University Medical Center then prescribed him antibiotics which also resulted in a relapse when he ate a slice of pizza. Finally, as a last attempt, he was prescribed probiotics to promote the growth of healthy gut bacteria and after a few months, he was able to incorporate carbs back into his diet.

 

 

 

Did you know that the body could produce its own alcohol? What are some other effects that an unbalanced microbiome may have on the body? 

 

 

 

How the “unknown” of the human gut microbiome gets in the way of metagenomic studies…

Did you know that the greatest concentration of bacteria lives in your gut? At two or three years old we have a balanced microbiome. While we know a lot about the human gut microbiome, there is a lot that is unknown about it. There has been a lot of improvement in finding an “unknown microbiome” for example, shotgun metagenomics enables researchers to take a sample of all genes in all organisms and allows them to find an abundance of microbes in many different environments.

What we know: 25 Phyla, ~2,000 Genera, ~5,000 Species, ~80% Metagenome mappability, and 316 million genes

What is unknown?: Undetected unknowns, hidden taxa and strain-level diversity (~20% sequences not matching microbial genomes), functional unknowns (~40% genes without a match in functional databases)

For example, one study where researchers studied a stool sample from 2 lean African men and a stool sample from 1 obese European. In the stool, they found 174 new species never seen in the human gut before and 31 new genome species (which can help in later studies). Found within these new species was, Microvirga Massiliensis which has the largest bacterial genome acquired from a human, along with Senegalvirus which is the largest virus in the human gut. We definitely know a lot more about the human gut microbiome than we did, even though there is a long way to go.

However, organizing large numbers of draft genomes from uncharacterized taxa is challenging, and while performing well for bacteria, assembly-based metagenomic tools are less effective when targeting new eukaryotic microbes and viruses.

The human gut microbiome intestines in an obese person vs. a lean person

To make improvements in uncovering “hidden strain-level diversity” it is vital to alter sample-specific associations from the metagenomes and to additionally incorporate as many genomes for each species in reference databases. Most species are “open”, meaning they don’t have an upper bound on the size of accessory genomes and it may seem impossible to reclaim all strain-level diversity; however, preserving “the effort of cataloguing strain variants remains crucial for an in-depth understanding of the functional potential of a microbiome.”

The difficulty is that the microbiome contains viruses. The “functional unknown” of the human gut microbiome is the broadest and most challenging to delve and study further into because there is little known about understanding its pathways and genes. There is one creation though, that helped try and find out what was “unknown” about the microbiome, called the Integrated Gene Catalogue. The Integrated Gene Catalogue of the human gut microbiome which consists of 10 million genes. It groups genes into thresholds, thus the genes then fall into sub-units of gene-families. Locating these genes is only a small part of finding out what they actually do. For example, out of 60.4% of the genes that were annotated, 15-20% of the genes have been discovered, but are stilled labelled “function unknown.” These results show how little is known about genes, their functions, and what is current in microbial communities. There is not enough investment in microbiome research. It is difficult because there could be viruses that can be discovered; however, not enough time is being put into finding it.

Lastly, there is a lot of research going into the human gut microbiome. For example, Fecal microbiome transplantation is where stool from a healthy donor gets placed into the other patients intestine, this transplant usually occurs when more bad bacteria take over the good bacteria in the intestine. However, it could cause more disease which is why further investigation in the human gut can solidify that transplantation could overall prevent a bad bacteria take over. The microbiome field is open to all technologies. Understanding the function of the microbiome still remains the largest challenge researchers face, along with the biggest challenge that “targeting specific genes are irreplaceable”, technology should be able to provide solutions (including microbial transcriptome, metabolome, and proteome, and the automation of cultivation-based assays to scale-up the screening of multiple taxa and genes for phenotypes of interest.)

 

How Dandruff Can Lead to Crohn’s Cures

The Intro

Crohn’s disease is an inflammatory bowel disease (IBD) that causes inflammation of the digestive tract. Symptoms can include abdominal pain, malnutrition, stunted growth, and more on the gross side, diarrhea. There is no known cure for the condition, but a research team under David Underhill, “research chair for inflammatory bowel diseases at Cedars-Sinai Medical Center in Los Angeles,” has made a promising discovery in the gut microbiome. The researchers’ observations involve a microfungus present in and on our bodies, but before we unpack their findings, let’s figure out why the heck there are fungi inside our bodies and how all this relates back to dandruff!

The Mycobiome

There is a vast array of microbes that make their home in and around our person. This collection of organisms is known as the microbiome. While our microbiome consists of thousands of different microbial species, a whopping “99.9% of the total number of microbial cells belong to only a few species.” That other 0.1% of microbes is known as the “rare biosphere,” and within this diverse collection of organisms lies the mycobiome, the assortment of microscopic fungi that inhabit each and every one of us. While the microbiome has received lots of attention, especially in our gut area, research on the mycobiome’s effects on the human body is just beginning. Underhill’s team’s discovery gives us a glimpse into just how impactful these relatively rare organisms can be.

The Dandruff

So, what does dandruff from our scalp have to do with the fungi in our gut, and how does all this involve Crohn’s disease? Underhill and his researchers studied Malassezia, a fungus pretty much omnipresent in and around our bodies. It’s been known that a concentration of Malassezia on our scalps causes irritation that leads to dandruff. However, this fungus also inhabits our digestive tract. The research team found that “people with Crohn’s had high concentrations of Malassezia on their intestine walls, while healthy patients had almost none. The researchers then demonstrated that simply adding this type of fungi to the gut — at least, in mice — was enough to exacerbate the inflammation seen in Crohn’s.” Therefore, the same fungal substance that can cause minor dandruff may also be heavily responsible for a serious IBD that affects about 780,00 Americans. 

The Significance

Even though some patients may achieve permanent remission, as we noted before, there is not yet an established cure for Crohn’s disease. However, Underhill’s team’s study raises some questions that could help shape the future of IBD medical development. Could the current expensive, 60% effective anti-inflammatory medicine be replaced with simple antifungal drugs? If we prove that reducing fungus reduces intestinal inflammation, then antifungal Crohn’s cures could be accessible and affordable for thousands of people! In 5th grade, I was diagnosed with Crohn’s, and while my condition has improved, it’s far from cured. It’s exciting to hear about new discoveries that could lead to advances in treatment to help people like myself. Underhill’s team and another team of researchers in Montreal have already begun clinical trials with antifungal drugs, so depending on their results, we may be one big step closer to curing Crohn’s and other inflammatory bowel diseases alike!

I think these discoveries are important and worth talking about, so if you have anything to add, challenge, or discuss, feel free to comment below! Thanks for reading!

 

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.

A Baby Beetle’s Nursery is.. In a Dead Mouse?!

Two Parent Burying Beetles in a Dead Rodent! Gross!

Typically, death for animals is experienced at the end of one’s life, but this is reversed for a certain species of carrion beetle, Nicrophorus vespilloides or burying beetle, in which infant beetles are born and raised within dead mice carcasses. In this mice carcass, parent beetles frequently tend to the dead animal by soaking it with their own oral and anal secretions, providing the baby beetle with a much needed dark microbial film. This bacterial goo actually closely resembles the parent beetle’s gut microbiomes, allowing for the baby beetle to truly thrive as an offspring of this beetle.

But why give these baby beetles this goo within a dead carcass? What benefit would that ever give to an insect?

In every living thing, there is sphere of personal bacteria that provide much needed life benefits as well as qualities like your own stench. Plus, bacteria can even join together through various forms of cellular communication, making an almost impenetrable microfilm biome for bacteria to live in, as seen in plaque on human teeth. This same function is what helps support infant beetles with necessary nutrients and life benefits by keeping the cadaver fresh and capable of sustaining youngster life. Plus, it even causes dead bodies to smell actually not terrible, but instead more pleasant! Crazy! “What burying beetle parents can do with a small dead animal is remarkable,” says coauthor Shantanu Shukla of the Max Planck Institute for Chemical Ecology in Jena, Germany.  “It looks different. It smells different. It’s completely transformed by the beetles.”

If these insects aren’t exposed to these microbiomes as a child, there could be some serious detrimental effects. As shown by Shukla’s lab work, larvae grown in cadavers that were swept clean of biofilm by Shukla and her colleagues used their food less efficiently and gained less weight (“roughly third less weight per gram than those who had their parents goo”).

But, the parents are not the only ones who manipulate the carcass, which can be seen here. As parent beetles and tended to their goo in the body and guarding their children, the infant beetles also add their own secretions to the dead mouse and also eat away the bacteria as well as the entire mouse body. “What will remain is the tail of the mouse,” Shukla says, “and the skull and a few pieces of skin.”

Isn’t it simply crazy how much bacteria can contribute to the growth of a baby insect as well as its impact on even a dead animal? Comment below about what YOU think about this!

How Non-Antibiotic Drugs May Affect the Human Microbiome

Scientists at the European Molecular Biology Laboratory (EMBL) in Germany tested 1200 medications on 38 types of gut bacteria to see if some non-antibiotic medications still affect bacteria. 835 of these medications were human-cell-targeting, such as anti-inflammatory drugs and antipsychotic compounds. Testing showed that around one-quarter of the drugs tested affected the growth of gut bacteria. The scientists are still unsure if this means that the drugs are harmful. The inhibition of bacterial growth could contribute to the drugs’ side effects, or even be “part of the drugs’ beneficial action.”

The scientists also found a connection between bacteria that weren’t affected by the medications and antibiotic-resistant bacteria, possibly showing a connection between the use of non-antibiotic drugs and the increase in antibiotic resistance, which is a major issue.

Nevertheless, this study advances how we think about medications and their effects on our microbiome, and helps us to understand our own bodies better.

Image result for antibiotics

Antibiotics

How The gut affects mental health

 

Image result for the gut microbiome

The article, Gut microbiota’s effect on mental health: The gut-brain axis, touches upon the way in which the gut microbiome is connected to your central nervous system and how they affect each other. It explains how the vagus nerve and afferent fibers connect your gut to your brain and helps control your mood by indirectly affecting the amount of Serotonin in your brain. An unhealthy microbiome or dysbiosis is correlated with a large number mental illnesses such as depression, anxiety, schizophrenia and bipolar disorder. It also mentions that the gut microbiome may also be able to affect your immune and endocrine system as well the central nervous system. The article concludes that the improvement of peoples gut microbiota may serve as an effective treatment for those with a number of mental disorders through the means of probiotics. The article Feeling Meh? This is How Your Gut Affects Your Mood(Plus, Exactly How to Fix It)  goes through an example of a man who dealt with serious depression and had tried antidepressants and felt only more unhappy while on them. He decided to change his diet instead to one high in vegetables and fiber as well as healthy amounts of protein and fat. The man felt he had more energy, he felt much less anxious and depressed and even felt he gained a much stronger sense of empathy which improved his relationships only furthering his happiness. Do you want to be Happier? Healthier?  Have a stronger immune system? Well then you better eat your probiotics and prebiotics. If you want to do some more research yourself check out this article: Article 2

Brain Disorder is Closely linked to… the Microbiome?

Parkinson’s disease and the gut microbiome. Two seemingly different topics are actually more related than meets the eye. 

Parkinson’s disease is a neurodegenerative disorder that effects dopamine-producing neurons in the brain. Physical effects of Parkinson’s include tremors, bradykinesia, and limb rigidity. Even though Parkinson’s is the 14th leading cause of death in the United States, the cause and cure remain largely unknown. 

However, a recent study done at the University of Alabama at Birmingham has discovered that there is a link between Parkinson’s disease and the bacteria in the gut microbiome. The gut microbiome contains tens of trillions of microorganisms that are apart of our immune system and metabolism. Approximately one third of the bacteria are common to most people, while the remaining two thirds are specific to oneself and their body. These organisms serve as our own “identity card” that makes us unique. Haydeh Payami, Ph.D., professor in the Department of Neurology in the University of Alabama at Birmingham School of Medicine who lead the study remarked that “the collective genomes of the microorganisms in the gut is more than 100 times larger than the number of genes in the human genome. We know that a well-balanced gut microbiota is critical for maintaining general health, and alterations in the composition of gut microbiota have been linked to a range of disorders.” More specifically, the microbiome helps rid the body of xenobiotics, or chemicals not naturally found in the body often arising from environmental pollutants.

Payami concluded that the research “showed major disruption of the normal microbiome … in individuals with Parkinson’s.” The study followed 197 patients with Parkinson’s from three distinct regions in the United States: New York, Atlanta, and Seattle. Research indicated that patients living in different regions had different gut imbalances, which may reflect the environmental, lifestyle and diet differences between the locations. The study also found that certain medicines used to treat Parkinson’s interact with the gut microbiome differently. It was also noted that the bacteria responsible for removing the aforementioned xenobiotics was different in individuals with Parkinson’s. However, it is still unclear whether Parkinson’s causes changes in an individual’s gut microbiome, or if changes in the microbiome are an early warning sign of the disease. 

The human gut microbiome from this source

Research between the gut microbiome and Parkinson’s is relatively new, so there are no concrete findings or cures yet. Fortunately, this study may hold information for assessing the efficiency or toxicity of medication for the disease by examining its effects in the microbiome. As someone whose relative battled Parkinson’s, I have firsthand witnessed the effects of this terrible disease. It is reassuring to see that there is new research being done every day to eventually find a cure, but in the meantime making the lives of those fighting Parkinson’s easier. As Payami said, “This opens up new horizons, a totally new frontier.”

To read the full study, click here. What do you think: Does Parkinson’s disease change the microbiome or is a change in the microbiome an early indicator of the disease?

Are microbiomes the real cause of arthritis?

It was thought that arthritis and joint pain afflicting obese people was caused by overstressed joints. However, an article from Genetic Engineering and Biotechnology News titled “Obese Microbiome May be the Real Cause of ‘Wear and Tear’ Arthritis” shows that the cause of arthritis is actually from inflammation driven by the microbiomes that live in the guts of obese people. The high-fat diet many obese people have unbalances the gut microbiome which in turn causes inflammation throughout their bodies, leading to very rapid joint deterioration. To solve the issue of arthritis, Micheal Zusick and his team at the University of Rochester Medical Center conducted an experiment on mice to see if a high-fat diet’s effects might be lessened with a prebiotic, a food that is high in fiber with the intention of improving the balance of microorganisms (in this case, microbiomes).

File:ArthriticKnee.jpg

In a healthy mouse gut, Bifidobacteria , a beneficial probiotic bacteria, is abundant. Probiotics are live microorganisms intended to provide health benefits when consumed, generally by improving or restoring the gut bacteria. However when a mice becomes obese, proinflammatory species gain in abundance. In the first part of the experiment, Michael fed mice a high-fat diet, similar to a “cheeseburger and milkshake” human diet, and after only 12 weeks of this diet, the experimental mice became obese and diabetic. They doubled their body fat percentage compared to control mice, which were fed a low-fat, healthy diet. As predicted, the colons of the obese mice were dominated by proinflammatory bacteria, and almost completely lacked Bifidobacteria. The changes in the gut microbiomes of the mice were in conjunction with signs of inflammation, as when the researchers induced osteoarthritis (OA) with a meniscal tear, a common athletic injury known to cause osteoarthritis, OA progressed much more quickly in the obese mice than in lean mice, as nearly all of the obese mice’s cartilage disappeared within 12 weeks of the tear.

Micheal then repeated the experiment but this time gave the mice the prebiotic oligofructose. What do you think is going to happen?

The results showed that the effects of obesity on gut bacteria, inflammation, and OA were completely prevented when the high-fat diet of obese mice was supplemented with the prebiotic. Prebiotics cannot be digested by rodents or humans, but they are welcomed for certain types of beneficial gut bacteria, like Bifidobacteria because colonies of those bacteria chowed down and grew, taking over the guts of obese mice and crowding out bad actors, like pro-inflammatory bacteria. This, in turn, decreased systemic inflammation and slowed cartilage breakdown in the mice’s OA knees.

Oligofructose made the obese mice less diabetic but it did not change the mice’s body weight. Obese mice who were given oligofructose remained obese. They had the same load of weight on their joints yet their joints were healthier. Reducing inflammation was enough to protect joint cartilage from degeneration. This shows that inflammation is the cause of OA and joint degeneration.

I think this topic is very interesting because arthritis can be very painful and can change a person’s physical life dramatically. Helping people to minimize the stress on their joints could allow them to get up and do activities they couldn’t before, improving their quality of life.

The United States Plays a Role in Changing our Bodies

Researchers at the University of Minnesota and the Somali, Latino, and Hmong Partnership for Health and Wellness have new evidence that the gut microbiota of immigrants and refugees rapidly Westernize after their arrival in the United States.

In order to accomplish this research, the researchers used a community-based participatory research approach from Minnesota’s large community of refugees and immigrants from Southeast Asian (particularly the Hmong and Karen people, ethnic minorities originally from China and Burma that mostly now live in Thailand). These immigrants and refugees were involved with designing the study.

A concern that has been relevant in the communities of refugees and immigrants was obesity. With this in mind, the researchers wanted to see if there is a relationship with immigrants and obesity.

The team of researchers compared the gut microbiota of Hmong and Karen people still living in Thailand; Hmong and Karen people who had immigrated to the U.S.; the children of those immigrants; and Caucasian American controls.

With this, the researchers found that there were significant changes in just the first six to nine months! The Western strain bacteroids began to displace the non-Western bacteria strain Prevotella. The more interesting part is that this Westernization continued to happen in the next decade, and so on. Overall, as the immigrants and refugees spent more time in the U.S., the diversity in the microbiome started to decrease. Indeed, the changes were even more pronounced in their children.

Overall, participants’ food logs suggested that eating more Western food played a role in changing the microbiome, but could not explain changes in the body, like obesity. So, we are still left with some wonder, but scientists will soon put our wondering to an end!

 

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!

 

You Can No Longer Blame Your Parents for Your Problems

Recently, researches have determined that it is not genetics, but the environment that shapes the formation of a microbiome will impact disease onset and progression.

What does this mean?

Eran Segal, a computer scientist and computational biologist at the Weizmann Institute of Science, and his colleagues went to Israel to conduct their investigation into where diseases truly come from. They chose Israel because of its genetically diverse population of Jewish people. In collecting blood and stool samples from over 1,000 Israeli adults from different backgrounds (i.e. Ashkenazi, North African, Yemenite, Sephardi, and Middle Eastern descent), researchers compared the different genetic profiles and ß-diversity of the microbiome samples of said adults. The results were shocking: genetics determined a “very small fraction of the variability that is seen across the microbiomes of people.”

To further prove the degree of which the environment influences the microbiome, Segal and his colleagues examined the microbiome compositions of related individuals, who never lived in the same household, and unrelated individuals, who lived together. The results showed that those who were unrelated and lived together had similar microbiomes, while those who were genetically related’s, but did not live in the same environment, microbiomes were different.

Why is this important?

Segal’s research proves that although some bacteria in the microbiome is heritable, they make up a small percent of the microbiome. Segal and his colleagues wanted to take their research one step further, and examine if host phenotypes can be predicted from microbiome composition. Instead of only using genetic data to predict a phenotype, researchers used both genetic and environmental factors, which gave them a more accurate prediction of a human phenotype.

For example, in a small study, they discovered that the microbiome contributed to 36 percent of the variation between people’s HDL cholesterol levels and 25 percent of the variation in their body mass indices. So maybe high cholesterol does not run in the family?

This study is very important in figuring out the most efficient way to fight diseases. It is vital to know which bacteria are not heritable, so that doctors can use the composition of microbiome to determine how to treat an illness. I believe that the combination of the microbiome, environmental factors, and genetics is key to understanding a disease, and knowing how to treat it. Since it has been discovered that environmental factors play a huge role in forming the gut microbiome, I am curious if scientists will use this information to control the environmental factors surrounding an infant, and see if that impacts any diseases said infant comes in contact with during its lifetime.

 

 

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?

Welcome to America, here is a risk of obesity?

Each individual has a personalized micro-biome with trillions of bacteria weighing about half a pound. We receive this microbiome at birth as a departing gift from our mothers, but this microbiome does not remain the same through the years. Studies by Dan Knights from the University of Minnesota have shown, however, that geographic location and diet results in shifts in our gut microbiota.

         Figure 1

 

So what does this mean?

The study by Dan Knight shows that immigration is causing dramatic shifts in new arrivals to the country. These new arrivals surveyed through stool samples are from places in Southeast Asia including 500 women of Hmong and Karen descent. These 500 women varied from individuals remaining in Thailand where most Hmong and Karen people live currently, first- and second-generation U.S. immigrants, and even included 19 Karen women followed through their first six to nine months in their new nation. All of these samples were then compared to 36 European Americans born in the United States.

On the microscopic level, the aforementioned immigrants are facing a shift in the gut microbiota from Prevotella bacteria to Bacteroides. “Prevotella bacteria produce enzymes that digest fibrous foods more common in Asia than the United States. In Thailand, the women ate more palm, coconut, a fruit called tamarind and the bulbous part of a plant named konjac.” This shift in bacteria causes a loss of 15% of microbiome diversity and furthermore does not shows signs of compensating for the loss of native microbes.

As the diversity shifts towards that of European American, obesity rates seem to spike among the population. The immigrants’ obesity rates increased by nearly six times, which is a drastic shift for the immigrants who held an originally low risk of metabolic disease. This shift, however, is still a complete mystery. The researchers cannot pinpoint the true cause as diet, location, medicines, water composition, or an unknown but there is a clear correlation between obesity and the lessened diversity in the gut microbiota. This correlation was discovered through an experiment involving mice injected with germs from obese women. These mice subsequently became heavier despite having the same food as their lean equivalents. Knight and his colleges plan to continue their studies in hope to possibly provide a solution to obesity through the injection of Prevotella, as they are driven by the intense sensitivity and stake of their subjects’ health.

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Figure 2: Experiment on Obesity with Mice

 

 

While immigration to the United States, a place of opportunity, may appear a blessing it does not come without risks. As the leading nation in obesity, it comes as no surprise that something is causing a drastic shifting in newly immigrated individuals’ gut microbiota and larger micro-biomes resulting in a higher risk of obesity. A gift and a curse, however, this phenomena has resulted in research that could possibly grant new insight on how to prevent obesity.

 

 

Kombucha: More Than Just a Trend

With its bitter flavor, supposed health benefits, vague origin, and aesthetic presentation, Kombucha has become the nation’s latest trend. In Williamsburg on a sunny day, you are bound to see someone sipping on this beloved probiotic tea. While hipsters, health nuts, and myself have all jumped on the Kombucha bandwagon, it seems that science is not too far behind. Researchers at McGill University have found that a combination of probiotics and an herbal supplement called Triphala led to 60% prolonged life expectancy in fruit flies.

This study suggests evidence that the gut microbiome and health may be intertwined, a notion widely believed in the practice of holistic health. Senior author of the study, Satya Prakash, stated “Probiotics dramatically change the architecture of the gut microbiota, not only in its composition but also in respect to how the foods that we eat are metabolized”.

Fruit flies have 70% similarity to humans in regard to their biochemical pathways, making the study promising for fellow Kombucha drinkers! The authors of the study cite the “gut-brain axis” , a communication system between the brain and microorganisms of the gut, as an explanation for their findings.

While Triphala may be hard to come by, some foods with a high probiotic content include sauerkraut, kimchi, kefir, yogurt, and of course, my personal favorite– Kombucha. So while it seems science may catch up, you and I can be well ahead!

Food For Thought!

 

A small fence separates densely populated Tijuana, Mexico, right, from the United States in the Border Patrol’s San Diego Sector. Construction is underway to extend a secondary fence over the top of this hill and eventually to the Pacific Ocean.

 

 

 

 

 

 

 

 

Here is some food for thought, what defines American Culture? Democracy? Freedom? As a matter of fact, for many immigrants, food is a defining factor of moving to the United States of America. Immigrants are fascinated by the combination of a wide variety and convenience of food. By the same token, the typical “American” diet is loaded with saturated fats, complex sugars and harmful chemicals. According to a recent Study from National Public Radio (N.P.R.), when immigrating to the United States of America, the typical “American” diet causes a completely new gut microbiome. The gut microbiome is the natural bacteria found in the digestive system that assist the body in a wide variety of tasks.

In order for N.P.R. to test this hypothesis, they gathered 500 ethnically Hmong & Karen women, residing in either Thailand or the United States of America. Of these women, they were either a first or second generation immigrant. After recording their findings, N.P.R. moved back to the United States of America, solely. When observing the gut microbiomes of the of caucasian Americans, the researchers concluded that the presence of Bacteroides leads to the decreased function of the gut microbiome. Next, 19 of the 500 women from Thailand moved to the United States of America. After many observation hours and careful logging of food consumed, the gut microbiomes of the immigrants began to diverge from their natural affinity. When reviewing the food logbooks, the scientists/researchers concluded/discovered that the typical “American” diet leads to the disruption of the gut microbiome because of its lack of fiber and over use of sugars.

Although this is not an urgent issue, this is an issue that must be addressed in the near future; this article exploits a greater issue for the United States of America. The United States of America is in desperate need to change its diet, consisting rich in fats and sugars, the population is facing serious medical issues such as obesity, cancer, high blood pressure and more.  This article demonstrates the effects of the typical “American” diet has on the United States of America. The United States of America must work quickly to collaborate with citizens and the private sector in order to make healthy alternatives to food, cheaper and more convenient, in order to mitigate health issues as well as promote preventive medicine.

Thank you!

From your favorite bacteria,

     SAMonella

 

 

 

Genetic Engineering on Gut Bacteria!?

E. coli on MAC – Photo credit to VeeDunn on flickr under Creative Commons License

Researchers at the Wyss Institute at Harvard University has successfully tested a genetically engineered signaling bacteria within a mouse’s gut. Having known that the many types of bacteria in the human gut can communicate through “quorum sensing” , researchers set to observe a particular type of quorum sensing, acyl-homoserine lactone sensing, which has not been observed in the mammalian gut. They wanted to test if using that particular type of signaling could create a genetically engineered bacterial information transfer system.

Using a strain of E. coli bacteria, they created two different colonies, each with a different genetic change: one was the “signaler”, it contained a copy of the luxl gene which produces a quorum-sensing molecule when activated, and the other was the “responder”, which contained a “cro” gene turning on a “memory element” in the responder.  This “memory element” expressed another copy the the pro gene, which allowed for the loop to continue, and the LacZ gene, which made the bacteria turn blue!

LacZ gene expression – Photo credit to Viraltonic on Wikimedia Commons under Creative Commons License

The researchers analyzed fecal samples of mice given signaler and responder E.coli and they were happy to see the signal transmission, blue coloring, was evident in the samples. This result meant that they had created a functional communication bacteria system in the mouse’s gut.

The researchers then repeated their experiment with a different type of bacteria, S. Typhimurium, as the “signaler” and E. coli as the “responder”, and they were pleased to see similar successful results.  They were able to successfully confirm that is possible to genetically engineer these communication circuits between different species of bacteria in the mammalian gut microbiome.

These tests are merely stepping stones for the bigger goal of creating genetically modified bacteria that will help humans in various different ways: detecting and or curing diseases, improving digestion, and so on. Isn’t it cool that something we barely realize is inside us has such a developed communication system that we might soon be able to cultivate more benefits from? What do you think would be some other benefits to be being able to genetically modify our gut microbiomes?

 

 

Does Immigration Alter the Microbiome?

Each human has our own microbiome; one that is unique to us. However, recent research has shown that the microbiome of someone’s body is not static, but highly subject to alteration. Microbiomes change depending on the atmosphere you are in- and they change very quickly, taking only nine months in the U.S. The University of Minnesota has found that, in people emigrating to the US, microbiomes “rapidly westernize”; aka, their native microbes are replaced with new ones. However, this shift in microbes is not equal- there aren’t enough new microbes to replace the old, resulting in a harsh decline in diversity; diversity that stimulates metabolism, digestion, and immune system development.

Dan Knights, a computational microbiologist at the University of Minnesota, states that in moving to another country, you pick up new microbes native to that country, and new disease risks as well. In this case, the shift in the microbiome makeup can be beneficial, as the new microbes may aid in defense against new disease. However, it has also been found that “Obesity rates among many of the study immigrants increased sixfold. Those who became obese also lost an additional 10 percent of their diversity.” This fact links diet shifts to microbiome shifts, yet Knights states that “diet alone wasn’t enough to explain the rapid Westernization of the microbiome,” and that other things such as water and antibiotic use factor in as well. However, diet is still an important part in microbiome health and diversity. Knights studied microbiota of Hmong and Karen women who had immigrated to the U.S., these immigrants’ American-born children, and white American controls. Their microbiomes shifted to Prevotella to Bacteroides, coming to resemble those of the white Americans who acted as the control. The immigrants’ children were even more susceptible to changes in and loss of microbial diversity.

Obesity statistics worldwide from the years 1996-2003.

We as Americans are highly aware of our obesity epidemic and are doing all we can to find a way to fix it. Research that links it to a cause relieves people- it provides hope that there is a way to change it. Knights remarks that “we do see that Westernization of the microbiome is associated with obesity in immigrants, so this could an interesting avenue for future research into treatment of obesity, both in immigrants and potentially in the broader population.” However, it cannot be used as an excuse for our problem as Americans- it is simply a breakthrough in a long journey that may help us in the long run.

Taking care of your gut might be a pain now, but is definitely worth it!

Brain with Alzheimer’s

The contributions of microbes to multiple aspects of human physiology and neurobiology in health and disease have up until now not been fully appreciated.
Many people have said the human gut is like a “second brain.” With trillions of microbes, the digestive tract of the human gut can influence many things such as your metabolism, nutrition, immune function, and even your happiness. New research continues to show links between the brain and the health of the gut.

For example, a study from Lund University found that “unhealthy intestinal flora can accelerate the development of Alzheimer’s disease.” Alzheimer’s disease is an extremely common form of dementia or memory loss. It is caused by the death of many brain cells, which progressively decreases the size of the brain and the number nerve cells and connections. This study showed that mice with Alzheimer’s have a different bacterial profile in their guts than mice without this disease. Dr. Frida Fak Hallenius said that “Alzheimer’s is a preventable disease and in the near future we will likely be able to give advice on what to eat to prevent it. Take care of your gut bacteria, by eating lots of whole-grains, fruits and vegetables.”

 

After these discoveries, researchers are looking deeper into how bacteria can affect brain pathology. One of their ideas is that the bacteria may affect T-cells in the gut, which controls inflammatory processes both in the gut and brain. Therefore, if we can find a way to increase the health of the gut, we can reduce inflammation and brain damage. Alzheimer’s, while it is one of the most feared diseases, is preventable to in extent and if not preventable, there are several ways to delay it. The human gut microbiome has a huge impact on your health and your brain’s health. If scientists can continue to discover how to make your gut as healthy as possible, Alzheimer’s could soon be a thing of the past.

http://www.huffingtonpost.com/entry/gut-bacteria-alzheimers_us_589e0e09e4b03df370d628be

http://www.nature.com/news/the-tantalizing-links-between-gut-microbes-and-the-brain-1.18557

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