BioQuakes

AP Biology class blog for discussing current research in Biology

Tag: microbiome

Hunter-Gatherer to Westernized Human Gut Biomes

Somewhere between the time of early hunter-gatherer humans, and the present-day humans living in modernized Western societies, the human gut biome lost much of its diversity. New research has contributed another clue as to the evolution of the human gut biome.

An international team of scientists studied the fecal samples of an intermediary group between hunter-gatherers and Westernized humans. The Bantu community in Africa is a traditional, agricultural population that has incorporated some available Western practices, including the use of antibiotics and therapeutic drugs.

 

Bantu people; Steve Evans,  https://commons.wikimedia.org/wiki/Bantu#/media/File:Mozambique001.jpg

The scientists compared the Bantu gut biomes to those of the BaAka pygmy population, who resemble early hunter-gatherer populations and have no Western influences, and to the gut biomes of humans living in modern, Westernized societies.

By analyzing the sequence data of the three human biomes, the scientists placed the Bantu’s biome composition in between the BaAka’s and Westernized humans’. The Bantu shared similar bacterial species as the BaAka, but lacked many of the traditional bacteria that the BaAka possessed. In fact, the BaAka had such a different biome composition that their gut more closely resembled wild primate biomes!

 

Based on the functions of the variable bacterial groups between the three populations, the team hypothesizes that the boosted carbohydrate-processing pathways in Bantu and American biomes is a result of the sugars in our diet, whereas the BaAka do not have much access to such foods and thus do not have such bacterial populations.

Ultimately, the scientists have accepted that our diet contributes significantly to our gut biome composition.

Possible Links Between Gut Microbes and Obesity, Cancer & Autism

While the bacteria in our gut play a vital role in the digestion process, recent findings have suggested that it could effect much more in our bodies. New studies have found possible links between the bacteria in our gut and obesity, cancer and autism.

Creative Commons image link

A study done by Cornell University and King’s College London revealed that Christensenellaceae minuta, a strain of gut bacteria, was found more often and in larger quantities in people with lower body masses. To investigate whether the bacteria is actually linked with obesity, researchers added the same bacteria into the guts of mice and compared their weight gain to mice lacking the bacteria. The research showed that the mice with Christensenellaceae minuta gained noticeably less weight than the mice lacking the bacteria. While research is still in its early stages, these results have made an exciting connection between bacteria in our gut and weight gain, which could dramatically impact the future of our health.

In addition to obesity, the bacteria in our gut has also been linked to cancer- in both beneficial and detrimental aspects. Researchers from the National Cancer Institute tested the effect of gut bacteria on chemotherapy in mice and found that the chemotherapy was significantly less effective in the mice lacking the bacteria. Similarly, another study found that cyclophosphamide, an antitumor drug, was less effective in mice with insufficient gut bacteria compared to those with normal levels. While these studies showed positive links between gut bacteria and cancer, other studies have found adverse effects of gut bacteria.

Unfortunately, a study published in The Journal of Cancer Research in 2012 has made a possible connection between Lactobacillus johnsonii, a strain of gut bacteria, and lymphoma, cancer of the white blood cells. The study claims that the presence of this specific strain of bacteria could lead to the development of lymphoma. Another study done in the UK in 2013 found that a specific gut bacterium, Helicobacter pylori, has the ability to deactivate the part of our immune system responsible for regulating inflammation. In effect, this could cause stomach cancer and ulcers.

While it may seem like a stretch, numerous studies have found a possible link to autism and the bacteria in our gut. A study done in 2013 by Arizona State University found that compared to children without autism, children suffering from autism had lower levels of Prevotella, Coprococcus and Veillonellaceae, three strains of gut bacteria. Even more surprisingly, another study revealed that the presence of Bacteroides fragilis in the gut reduced autism-like symptoms in mice. Research in this field is still in its primary stages, as researchers are trying to figure out if these connection are in fact related, and if so, how the bacteria directly effects these conditions.

 

New Reason to Watch Your “Diet”: The Human Gut Microbiome and Competition

The human body consists of approximately 100 trillion microbes, and in the digestive tract of the human gut alone it is estimated that there are trillions of microbes. Recent studies done by Athena Aktipis, a researcher at Arizona State University’s Biodesign Institute, have shown that people’s dietary choices either help to increase the cooperation between gut microbes and their human hosts, or they could potentially lead to conflict between the two.

The microbiota consists of bacteria, and the human microbiota contains about 500 different species of microbes. There is a possibility that the composition of these microbes could affect behavior, susceptibility to allergies, and even likelihood for obesity. According to several previous studies, exposure to intestinal bacteria prevents allergies in infants and young children. This has been determined by examining the noticeable difference between the compositions of intestinal bacteria in children who have developed allergies and children who have not. The current study further looks at cooperation and competition between human cells and other cells that coexist with them. Cells are cooperative between the human cells and gut microflora when bacterial cells produce energy and vitamins. It also is beneficial when bacterial cells help to detect pathogens that are dangerous to the host. Conflict on the other hand is more likely to occur when the needs of microbes and the needs of the host are at “cross-purposes”, or they contradict one another. This internal conflict could lead to chronic afflictions such as inflammatory diseases that are caused directly by the body’s attempt to maintain dominance in this “power-struggle” within the host.

These recent studies have also shown that sugar and fat are most likely contributors to conflicts that arise between host cells and microbes. This is due to the fact that fats and simple sugars also can be used by microbes such as E. coli, which further contributes to the conflict. The results of these studies suggest that a diet consisting of low fiber and abundant sugar leads to the conditions where conflict takes place between human cells and microbes. When their interests clash or coincide, the cells in the body trigger immune responses that lead to different afflictions that include a wide range of diseases, some of them being inflammatory. Similar to fats and simple sugars, iron is also potentially dangerous in the sense that a pathogen could steal iron from host cell proteins which would ultimately compromise the health and nutrition of the host. According to the studies, it is recommended to maintain a diet that has high nutritional density but also low concentrations of pathogens in order to promote cooperation and prevent any competition or conflict that could damage your overall health and wellness.

 

Further reading:

Gut microbiota in 2016: A banner year for gut microbiota research

The Effect of Diet on the Human Gut Microbiome: A Metagenomic Analysis in Humanized Gnotobiotic Mice

More Bacteria than Human?

The well being of humans is best when we are cooperating with others whether that be other humans or bacteria inside of us. According to Matthew Bull “the human gut microbiome and its role in both health and disease has been the subject of extensive research, establishing its involvement in human metabolism, nutrition, physiology, and immune function.” An imbalance in our microbiome will often result in some type of sickness so it is very important to keep our guts healthy. It is likely that there are more bacteria cells in our gut than there are our own cells. So in this image right here  there would be more bacteria cells than human cells. Some people even consider the microbiome a bacteria ecosystem that just happens to be in our gut. While this may sound bad, these bacteria often break down food for us and supply us with energy needed to do daily activities. It is truly fascinating to think that we have many living things inside of us that may even outnumber what is actually considered “us”. But is it possible for these bacteria to take over our bodies? The answer is probably no…we hope, but if we continue to eat well and stay healthy these bacteria should continue to help us. However, if we eat poorly and don’t stay healthy these bacteria can end up being a problem for use. So at the end of the day eating health helps the relationship between us and the bacteria inside of us stay healthy and lets us stay healthy.

The diet that we should have to keep a healthy relationship with these bacteria involve eating less sugar and fat and eating more fiber. A diet with a lot of fat and sugar but little fiber can lead to illness. It is also best to stay away from eating a lot of iron. There are some things that help our microbiomes such as milk, milk has proteins in it that help keep our microbiomes health. So eat less sugar, bad fats, and iron and eat more fiber and drink more milk.

 

The Microbiome’s Role in the Success of a Diet

Just in time for the many New Years resolutions where people promise to go on a diet to lose weight or get healthier, a new study covered by Huffingtonpost has found that the bacteria in your gut can affect the success of your diet.  This new research has demonstrated that all the diet alterations in the world, whether you give up pizza or ice cream, may do nothing if your intestinal bacteria are out of whack from a life of eating poorly.

Originally published in the journal Cell Host and Microbe, these new findings tell us that switching to a healthier diet may not help much, at least in the beginning, if you still have unhealthy bacteria left over from your non-diet days.

However, according to Dr. Jeffrey Gordon, a biologist at Wash U in St. Louis and senior author of the paper, the scientific community has found a way to “mine the gut microbial communities of different humans to identify the organisms  that help promote the effects of a particular diet in ways that might be beneficial.” In simpler words, research has shown that short-term dietary changes can alter the gut microbial community.

In order to demonstrate these findings, the researchers examined two groups: one that ate the standard, high-calorie American diet and one that ate a more plant-based, lower calorie diet. As expected, they found that those with the standard American diet had less diverse microbiota and that people with a plant-based diet had a more diverse, and healthier, microbiome. Diversity in the gut is important because it aids digestion, nutrient absorption, and immune system function; on the flip side, an unhealthy microbiome can contribute to inflammation, anxiety, depression, poor digestion and even autoimmune diseases.

Link to Image

The next step in the experiment involved analyzing the microbiome set-up in mice who had been colonized with bacteria from the human subject. These mice were either fed the native diet of their human donor (American or healthy), or the opposite diet. Analysis of the results revealed that all mice saw a change in their bacteria in response to the diet, but the bacteria of the American diet showed a weaker response to being changed to a plant-based diet ― their microbial communities didn’t increase and diversify as much as the mice colonized with the bacteria of the humans who ate a plant-based diet.

In conclusion, your gut would definitely benefit from a diet more heavily based on plants and vegetables, but if you have been eating a very unhealthy diet thus far, it may take a little longer to see results, as the makeup of your internal microbiome has to change.

Evolution of the Human Gut Microbiome

NIH Image Gallery Image Link

According to an article on Science Daily, Westerners have a very different human gut than hunter-gatherers. Research suggests that Westerners tend to have a less diverse human gut. However, the reason for why is still unclear. Researches from this study have observed two particular groups of people. The hunter-gatherers, known as BaAka pygmies, relied on foods such as fish, fruits, and vegetables. Whereas the group of Westernizers, the Bantu, relied on a market economy. The Bantu grew fruits, other plants and raised goats. They also used antibiotics and therapeutic drugs available.

The results of the study revealed that while the  BaAka and Bantu gut microbes were from similar bacterial species, the abundance of traditional bacterial groups was decreased in the Bantu. When researchers delved into what could have caused the difference between the two groups, they found that diets are the most important driver of microbiome composition in humans.

Another study done by evolutionary biologist, Andrew Moelle, suggests that humans and animals have inherited some bacteria from their ancestors. Moelle studied three types of bacteria living in the feces of wild chimps, bonobos, gorilla and a group of people from Connecticut. He concluded that 2 of the three bacterial trees matched primate relationships. Moelle also expressed how these relationships are getting harder to study due to the effect that industrialization and antibiotics have. They have reduced the diversity of bacteria living in and on humans.  Microbial geneticist, Julia Segre, expressed that humans have been exposed to antibiotics and modern life and as a result, Wild African apes might “still have their ancient gut flora, but the people in Connecticut might not.

A study done by Howard Ochman found that human guts most closely resemble the gut of a gorilla. Like the other researchers, Ochman acknowledges that as a result of modern humans there is a loss of microbial diversity. He also explains how this can be a problem because humans have lost a number of bugs that help digest plant matter. However, humans have gained others that help digest meat.

 

The Human Gut Microbiome and Autism Spectrum Disorders

Researchers of the human gut microbiome have made connections to the autism spectrum disorder.  A gut microbiome involves the digestive tract microbes.  To learn more general information click here.  Studies tested DNA of children with gastrointestinal complaints.  Researches compared children with Autism Spectrum Disorder, and mainstream children.  It was found that children with Autism Spectrum Disorder had too many Clostridium or Desulfovibrio clusters.  To learn more about these gene clusters click here. Developing fever, receiving oral antibiotics, or ingesting probiotics are all likely to alter the gut microflora.  When children with Autism Spectrum Disorder do the above, they have exhibited improvement in their gastrointestinal pains; however, there hasn’t been scientific research, as it has only been found anecdotally. Research has been limited due to the difficult culture-dependent techniques; however, metagenomic technology could be used to discover and reduce the effects of the gut microbiome as a part in Autism Spectrum Disorder.

A longitudinal study completed in May 2016 shows more progress that scientists have made in discovering different aspects of autism in relation to the microbiome.  For two weeks, stool samples were collected from patients with autism and their siblings without autism in order to be compared. Sarcina ventriculi, Barnesiella intestihominis, and Clostridium bartlettii are organisms that are related to autism. They were found in the stool samples of children with autism, but not their siblings. Gastrointestinal symptoms were reported on days 6-8 of the study for children with Autism Spectrum Disorder, where Haemophilus parainfluenzae was detected at the onset. These patients also exhibited behavioral challenges during these days.

Though scientists have not found a diagnosis for Autism Spectrum Disorder yet, it is clear that the gut microbiome plays a role in the development. Further research that is not merely based off of a handful of patients needs to be completed to learn more.

Photo of Gut Flora

Sometimes less is better. Especially in the case of germs.

Scanning electron micrograph of Escherichia coli

Photo by NIAID

Apparently we’re healthier than we thought!!

Throughout the 20th century, scientists who studied the microbiome had thought that humans contain around 9000 times more germs than human cells.  Scientists now believe, however, that that number is more like 30 percent.

Micro biologists: Ron Sender, Ron Milo, and Shai Fuchs took on the challenge to actually find out the ratio of bacteria to cells in the human body.  First, its important to know the types of cells that make up the human body.  One might think that muscle and fat cells make up the largest portion of human cells in the body but that is wildly incorrect.  In fact, despite their weight and size dominance, they make up a measly .2 percent of the body’s cells while blood cells make up 90 percent (mostly red blood cells).

The colon houses the most bacteria in the human body by a long shot.  This makes sense as it is the pathway for human feces out of the body and reaches up to 5 feet in length.  The “trio” of scientists estimate that the human body contains somewhere between 30 trillion and 50 trillion cells and that the bacterial count is around 30 to 60 percent higher than the amount of cells.

Now, despite the insightful findings of Sender, Milo, and Fuchs, the microbiome community still has a lot of research to do into the subject of germ:cell ratio in humans and scientists believe that the trio missed some important factors in their experiments and as geneticist Julie Segre points out, “Other researchers also point out that the new paper’s calculations focused on bacteria. Yet the body can host other types of microbes as well. Those include viruses, fungi and archaea (Ar-KEE-uh). Viruses tend to vastly outnumber bacteria, so they could skew the microbe-to-human cell ratio upwards.”

The most important and prevailing part of the trio’s research was that the amount of bacteria that we have in our body and attached to human cells is much less than we had previously believed.

https://student.societyforscience.org/article/cell-recount-people-host-far-fewer-germs?mode=topic&context=79

Original Article 

Trust Your Gut and Exercise

 

File:Wild garden of the gut bacteria 5.jpg

According to an article on GEN news, the level of Microbiomes contained within the Gut is influenced by exercise as a young child. Microbiota are the organisms that share our body space, and the gut has a particularly concentrated region of these organisms. Scientists estimate that gut microbiomes make up anywhere from 1-3% of total body mass. As it turns out the saying, “trust your gut” has some scientific merit. Microbiomes promote healthy brain function and promote anti-depressant effects, as well as adding up to 5 million genes to the human genome. Having a healthy gut is a key to overall biological health.

A recent study by Colorado University claims a connection between early life exercise and healthy microbiome activity. This study was conducted with rats, with one group young of rats exercising daily contrasted against a control of rats who behaved normally. The younger exercising rats experienced a growth of probiotic bacteria in their guts, more so then the stationary rats or even older rats who exercised. Researchers “emphasize the ability of exercise” to promote a healthy brain and metabolic function. In the future, Colorado University will look for ways to promote healthy microbiome activity in adults who have a much more stagnant microbiome structure.

 

Sources:

1.http://www.genengnews.com/gen-news-highlights/gut-microbiome-influenced-by-early-life-exercise/81252160/

2.http://learn.genetics.utah.edu/content/microbiome/

3.http://patient.info/health/the-gut

 

Overload of Calories

You may not realize this, but we lose a significant amount of calories while we are asleep. Now imagine if the calories we burned while resting or sleeping did not get burned. If those calories did not burn while we were asleep it could cause us to become obese much more easily. The process of our metabolism rates getting slower does not occur until later on in most people’s lives. Unfortunately, those who have to take antipsychotic drugs may approach this problem sooner than expected.

Risperidone2D.svg

 

 

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New research has been found by the University of Iowa Health care that an antipsychotic drug, risperidone, effects people’s metabolism rates. The reason why is due to the gut microbiome going through an alteration through it’s bacterial anatomy. Kirby Carlarge, University of Iowa pediatrician,  and Justin Grobe, University of Iowa professor in pharmacology, worked together to test mice on risperidone. After two months the mice on risperidone gained an extra 2.5 grams compared to the control group of mice. Carlarge and Grobe used the total calorimetry machine to understand whether aerobic-resting states or non-aerobic resting states in terms of metabolism have been affected. The total calorimetry machine is able to give the exact measurement of the total energy change by inputting exact amounts of oxygen into the mice, outputting exact amounts of carbon dioxide, and the reaction of heat production. The results were the aerobic-resting metabolic rate to remain the same, but the anaerobic-resting metabolic rate had decreased . Therefore, the shift in the mice’s microbiomes does not affect the aerobic-resting metabolic rate, but instead affects the anaerobic-resting metabolic rate.

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Risperidone draws a connection to weight gain due to the alteration in the bacterial anatomy of the microbiome. However, despite this understanding of risperidone there are no definite ways of preventing this situation occurring. Therefore, it is very likely for patients undergoing this treatment to become obese. Do you think there are other variables that could change and prevent risperidone creating this effect?

We Eat What We Are: The Importance of Microbes in Our Gut

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Photo of microbes (licensing information here)

Ever since the discovery of the microbes, scientists have become very aware of the miniature world of microbes. This early awareness was later translated to an understating of how bacteria and other microbes effect the world we live in. Of course, early scientific and medical research often focused on microbes that cause diseases and how to treat them. However scientists have become aware that each individual is in fact a biome of microbes living on our exterior and inhabiting our interior organs.  Bacteria also play an important role in digestion helping us break down certain foods, producing vitamin and allowing for efficient absorption of nutrients. Increasingly, investigators have began exploring how the micro biome in our digestive track impacts our health and wellbeing.

Gut bacteria appear to play a role in matters of obesity, the development of certain types of cancer and ulcers. They do so by producing certain chemicals that affect a variety of health outcomes. Gut bacteria also produce a wide variety of neurology related chemicals that affect mental processes such as depression and anxiety disorders. Some studies now point to a relationship between autism and particular levels of gut bacteria.

The recognition of the importance of gut bacteria in health and disease have implications in a number of areas. First of all it suggests that a healthy diet should involve the encouragement of the development of good gut bacteria. It also suggests that gut bacteria diversity is a positive goal. Lastly, the results of many of these studies of the significance of gut bacteria in regard to disease point to the need to incorporate the study of an individuals gut bacteria as part of the treatment regiment to fight particular illnesses

 

 

Possible Connections between the Gut Microbiome and the Brain

It is not a new concept that gut bacteria affects a person’s health. But this article published in The Atlantic explains how they may even affect the human brain. Some researchers believe that the microbiome may play a role in regulating how people think and feel. Scientists have found evidence that this community of bacteria (trillions of cells that together weigh between one and three pounds) could play a crucial role in autism, anxiety, depression, and other disorders.

500px-E_coli_at_10000x,_original

 https://en.wikipedia.org/wiki/Fecal_bacteriotherapy#/media/File:E_coli_at_10000x,_original.jpg

Much of the most intriguing work has been done on autism. For years, it has been noted that about 75 percent of people with autism also have some gastrointestinal abnormality, like digestive issues or food allergies. This has prompted scientists to search for potential connections between the gut microbiome and autism; recent studies find that autistic people’s microbiome differs significantly from those of control groups. Caltech microbiologist Sarkis Mazmanian specifically focuses on a species called Bacteroides fragilis, which is seen in smaller quantities in some children with autism.  Mazmanian and several colleagues fed B. fragilis from humans to mice with symptoms similar to autism. The treatment altered the makeup of the animals’ microbiome, and more importantly, improved their behavior: They became less anxious and communicated more with other mice.

Perhaps the most well-known human study was done by Emeran Mayer, a gastroenterologist at UCLA. He recruited 25 subjects (all healthy women) for four weeks. He had 12 of them eat a cup of commercially available yogurt twice a day, while the rest didn’t. Yogurt is a probiotic, meaning it contains live bacteria. In this case it contained four species: bifidobacterium, streptococcus, lactococcus, and lactobacillus. Before and after the study, subjects were given brain scans to gauge their response to a series of images of facial expressions—happiness, sadness, anger, and so on.

To Mayer’s surprise, the results showed significant differences between the two groups. The yogurt eaters reacted more calmly to the images than the control group. “The contrast was clear,” says Mayer. “This was not what we expected, that eating a yogurt twice a day for a few weeks would do something to your brain.” He thinks the bacteria in the yogurt changed the makeup of the subjects’ gut microbes, and that this led to the production of compounds that modified brain chemistry.

As scientists learn more about how the gut-brain microbial network operates, they think it could be manipulated to treat psychiatric disorders. And because these microbes have eons of experience modifying our brains, they are likely to be more precise and subtle than current pharmacological approaches, which could mean fewer side effects. “I think these microbes will have a real effect on how we treat these disorders,” neuroscientist John Cryan says. “This is a whole new way to modulate brain function.”

Love and happiness really do come from the bottom of your… gut?

Serotonin is the famous neurotransmitter oft attributed to causing joyous type emotions.  Unlike most neurotransmitters, which are produced predominately in the brain and nervous system, a recent study mentioned in a review article estimate that, “90 percent of the body’s serotonin is made in the digestive tract. […] [C]ertain bacteria in the gut are important for the production of peripheral serotonin.”

uBiome - Microbiome Sequencing Gut Bacteria Sample Kit

 

Interesting play on words of the “Microbiome.” The gut microbiome comprises most of our body but very little of our mass… It outnumbers our cells 10 to 1! [Source]

 

Researchers at the California Institute of Technology (Caltech) sought to identify a link between the gut microbiome and the production of the serotonin neurotransmitter. Peripherally made serotonin is already understood as a product of the digestive tract, however, is there a link between the myriad of bacteria that compose our gut microbiomes and the neurotransmitter? What they found, was surprising; notwithstanding the known communicative link between the nervous system and the microbiome, the researchers found that the microbiome is not directly responsible for most of the production of the neurotransmitter.  The bacteria interact and stimulate the production of serotonin by the intestinal cells.

 

To arrive at this conclusion, the researchers studied the effects of “germ-free” mice.  They found that the mice that exhibited a dearth of flora within. Experimental results indicated that the mice produced around 60% less serotonin than mice with normal gut microbiomes.  The experiments also demonstrated an interesting result that may lead to future studies on the serotonin deficiency treatments–the researchers found that when augmenting the gut microbiomes with bacteria responsible with serotonin production stimulation, the levels of the neurotransmitter increased. Of course, the subject is vastly complicated, and will therefore require extensive research to more fully understand.

Original Article

Study from Article

Serotonin Wikipedia Page

Image Source

You Are What You Eat

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Original Link To Image: https://www.flickr.com/photos/pnnl/8146322408

It has been known for some time by scientists that variations in food intake lead to various different gut floras.  However, that theory had only been tested on mice…Until now.  Lawrence David, assistant professor at the Duke Institute for Genome Sciences and Policy, led an experiment that resulted in the discovery that different foods not only lead to different bacteria, but the bacteria themselves experience gene variations.  Although the discovery itself is truly amazing, the celerity at which the changes occur is the most impressive.  University of Chicago’s professor of medicine Eugene Chang specializes in gastroenterology originally thought the changes would take months or even years but the study showed that the changes started to take place within a couple of hours.  There were also changes in the amount of bile acid secreted into the stomach and that microorganisms native to cheeses and cured meats were stronger against this.  The real question is “Why is this relevant?”  To Chang, the first is evolutionary.  Ancient humans who experienced rapid dietary changes could successfully switch from nuts and berries to meat with little gastric distress and maximum absorption of nutrients from even the most unrecognizable foods.  The second is the effects of diet on certain diseases.  Chang, who has been leading a research team to discover the connection between  B. wadsworthia and colitis in mice is yet to apply these tendencies to humans.  However, he believes there could be a connection.  His experiments show just how sensitive the body is to dietary change.  Dramatic changes in ones diet could lead to a brief exposure to harmful diseases such as inflammatory bowel disease.  The experiments are difficult to conduct however because according to David, it’s hard to find even 10 people willing to dramatically change their diets for science.

original article: http://www.scientificamerican.com/article/the-guts-microbiome-changes-diet/

similar article on the gut micro biome: http://www.medicalnewstoday.com/articles/290747.php

Using Poop to Save the People

     Bi YO! What’s going on readers? Today I will discuss the recent phenomenon of gut microbiome transplants, and more interestingly, how recent research has allowed patients to be treated through the use of human feces.

Our microbiome, a term coined by Joshua Lederberg, is a system used “to signify the ecological community of commensal, symbiotic, and pathogenic microorganisms that literally share our body space and have been all but ignored as determinants of health and disease.” They are the bacteria insi

Microbiome Chart Explanation (https://commons.wikimedia.org/wiki/File:Microbiome_analysis_flowchart.png)

de of us and are vastly abundant in our body. A Clostridium Difficile infection causes diarrhea and the colon to be inflamed. However, there had not been a truly successful treatment to this issue until recently. But recently, the poop of the people has proven itself to be a powerful panacea. Ari Grinspan became performing FMT’s, fecal transplantations, in 2013, and has done so with a 92% success rate. In these procedures, feces is taking from a healthy, clean donor. It is vital that this happens. Then, they transfer the healthy sample into the colon of the unhealthy patient while the patient is undergoing a colonoscopy. Scientists are actually currently uncertain of why it works so well- one theory is that increased bacterial competition stops growth of Clostridium Difficile. Regardless, the process is groundbreaking- maybe it wasn’t waste after all.

Junk Food Encourages Disease

According to a recent discovery posted in Science News, a typical American diet, consisting of poorly nutritional foods, leaves one prone to getting sick by weakening their immune system. Interestingly enough, this issue is rooted in cells that are not your own. In your gut microbiome, there are countless varieties and numbers of bacteria, all working away at the food that passes through your gut. Now, these bacteria are actually quite manipulative, and besides from feeding off of the food that you eat, teach your immune system what to attack, like an instructor or tutor for your immune system, albeit a biased one. These bacteria have colonized your body. They’re not just going to let some pathogen get in the way of their free meal ticket.

(What it looks like in there)

What happens when you eat certain foods, like junk foods, is that your gut microbiome changes. Different bacteria thrive on the fatty or sugary foods while other bacteria that survive off of more complex starches and carbs fade away, changing the demographic of your gut microbiome. This limited variety also limits the amount of invaders your immune system knows as hostile, or understands how to deal with, and therefore, you are more susceptible to disease, or medical complications.

(Actual photo of a biofilm found in the gut)

This was proven by taking samples from fit and obese humans and inserting them in otherwise sterile mice. Their resulting microbiomes grew, and the mice with the obese implant suffered more medical problems than the mice with the fit implant. This is because there were not enough “trainer” bacteria in the first mice’s gut to help train it to fend off disease, and thus it got sick more easily. So don’t go blaming your immune system the next time you get sick. It may be your fault for avoiding real, nutritional food (not just salad), and not taking care of it.

The moral of the story is to eat your vegetables and serve the bacterial overlords that have taken host in your body.

They’re good for you.

Trust me.

 

Asthma From The Gut

Asthma is a a disease without a cure. Unfortunately, it is spreading rapidly throughout the world.  With asthma, a person’s lungs do not function normally, and the lungs are a key part of the immune system.Asthma is related to a hyperactive immune system, a system that is gut-centric. Since it can not be cured, the best we can currently do is try to identify it’s causes. This can be very challenging and scientists do not know much about the bacteria inside of us. Being gut-centric implies a direct relationship between the gut microbiome and the immune system.

Asthma Inhaler

Image courtesy of NIAID on Flickr

Recently, a team of scientists proved this direct relationship. Their study discovered that the abundance of FLVR bacterium in a baby’s gut can affect their likelihood of being diagnosed with asthma. The study showed how Canadian children with low levels of FLVR in their feces when they were three months old proved much more likely to get asthma. By the time they reach age one most kids have the same levels of FLVR, this shows how key the timing is. The study then provided mice with extra FLVR, and tried to induce asthma. But, instead of getting inflamed lungs, the mice continued to breathe normally. This displays a potential solution. Scientists now believe that in those first three months of life, FLVR is necessary to properly train the immune system.

I chose to do this study because asthma is a disease that rapidly affects more and more people. The study, discovering a new cause of asthma holds promise. This suggests a possible future cure for asthma. If scientists can use antibiotics to perhaps enhance the levels of FLVR in the early days of children’s lives, perhaps asthma can be cured. This study of the different types of bacteria in the immune system is especially interesting due to our unit on the structure of different types of cells. Learning about the greater, medical application of this particular type of bacteria is especially fascinating. Please feel free to comment below with any thoughts or questions you have regarding this topic.

The original article can be found here. 

Sewage Does More than Just Gross You Out… It Carries a Signal For the Microbiomes of Humans

Who knew that sewage would ever be useful. Well, it is a successful way to collect fecal bacteria from people. It can monitor, through gut microbes, the public health of a population without invading people’s privacy. The human gut microbiome consists of huge amounts of bacteria in the gastrointestinal tract. This gut bacteria has important functions in a healthy human. Recently, there has been much attention to the human microbiome, and more specifically, finding a “healthy microbiome” by identifying which bacterial communities are associated with healthy individuals. What has been hindering this experiment are financial concerns but also privacy concerns in terms of the individuals that can be screened.

Researchers from MBL (Marine Biological Laboratory) and the UWM (University of Wisconsin-Milwaukee) School of Freshwater Sciences proposed the idea of using sewage as a population that consists of a signal for human microbiomes. The scientists used oligotyping to compare 137 healthy people’s gut bacteria (provided by the Human Microbiome Project) to the bacterial communities of more than 200 sewage samples from 71 different U.S. cities. Researchers realized that geographically distributed populations consists of a similar core set of bacteria and its members symbolize many different communities within U.S. adults. The percent of obese people in a city is used by the study as a measure of a lifestyle difference which indicates that this bacteria community structure is accurate in detecting obesity in a city. Lifestyle differences are important because they can change the human gut microbiome and an indicator of obesity is the microbial community composition. This process of working with microbiomes of individuals is similar to drawing a map of a specific geographical area and fishing out new understandings and patterns. If it weren’t for the sewage, the scientists wouldn’t have been able to differentiate the cities based on their level of obesity. This type of approach can be effective when it comes to answering concerns about public health, without undermining the privacy of individuals.

I found it interesting how this profound yet relatively small experiment is even part of a bigger plan to create better water pollution and public health assessments. Do you think it can lead a better water pollution and efficient public health assessments? Overall, it’s amazing how new technologies can aid in decrypting information from complicated environments. I’m excited to see where this experiment takes us as it leads researchers and scientists in a more knowledgeable outlook on our environment and in public health.

The original article can be found here.

Diet Tip #1: Hang Out with Skinny People and Go on a Low Calorie Diet

labrat

Microbiomes are incredibly vast and mysterious; we don’t quite know how they work. However, with a few experiments, we have come to a few conclusions.

1) Microbiomes determine your weight.

Scientists extracted bacteria from the intenstines of human twins, one lean and one larger. The injected these microbiomes into twin mice. The mouse who received the large twin’s microbiome gained fat and the mouse who received the lean twin’s microbiome remained small.

2) Fat microbiomes can be influenced by a skinny microbiome.

A fat mouse placed in a cage of skinny mice lost weight.*

3) Skinny microbiomes cannot be changed.

A skinny mouse placed in a cage of fat mice remained skinny.*

4) With the correct diet, you can become skinny.

Fat mice eating healthy food made them skinny but when they ate junk food, they stayed fat. A different group of scientists replicated this experiment with overweight humans and a low calorie diet. Their microbiotic diversity was low and increased significantly, leading to weight loss.

5) Diet does not affect skinny people.

Regardless of which diet the skinny mice ate, they stayed skinny. A different group of scientists replicated this experiment with skinny people and a low calorie diet. Their microbiotic diversity was already high and did not change much.

*read the full study here

Why?

Fat microbiomes tend to be more efficient at extracting nutrients from food and storing the excess, so whenever someone with an efficient microbiome eats, he/she stores a lot of the nutrients. Skinny microbiomes, on the other hand, are not as efficient at extracting nutrients so there is less energy to store after a meal. Going on a low calorie diet if you want to lose weight could solve the problem because whatever can be extracted from the food will be used for day to day functions. Considering that skinny people already are not extremely efficient at extracting nutrients, a low calorie diet will not necessarily cause any significant changes.

This source performed a study (humans) where they discovered that obese people typically have lower genetic diversity than lean people. Obese people who went on a low calorie diet had a higher genetic diversity at the end of the experiment than those who did not go on a low calorie diet, and obese people who continued to have a low genetic diversity gained significantly more weight over nine years. Lean people who went on a low calorie diet did not have a significant increase in microbiotic diversity compared to lean people who did not go on that diet. However, this correlation does not imply causation because some obese people have a high genetic diversity. Scientists believe that a low genetic diversity is linked to metabolic disorders, which could cause obesity, but that obesity in and of itself is not always caused by low genetic diversity.

Whenever you touch, breathe, or eat something, bacteria is entering your body and interacting with the native bacteria. So, when fat mice interact with skinny mice, it’s possible that the fat mice pick up diverse bacteria from skinny mice, contributing to their increase in microbiotic diversity, and when skinny mice interact with fat mice, they can’t lose genetic diversity but also have nothing really to gain from mice with low genetic diversity.

Conclusion: If you have a metabolic disorder, it could be beneficial to surround yourself with skinny people and eat low calorie foods because you’re more likely to absorb diverse types of bacteria while also storing less energy from food.

Are Antibiotics Killing More Than Just Infections?

What are in your antibiotics?

We all take antibiotics. Staph infections, Strep throat, etc. and they get the job done. Within two or three days, sometimes a week, you’re cured and infection-free. But is that really best for us?

Microbiomes are what make us so unique and individual. In fact, we have more bacteria cells that human cells in a 10 to 1 ratio. We have different microbiomes for different parts of the body; our mouth has a different microbiome than our skin microbiome which has a different microbiome than our gut microbiome. We can influence our microbiomes by what we eat, or rather they influence us based on what we eat. As part of an evolutionary benefit, our microbiomes adapt to newly introduced food within days, which we previously thought took years to change. In other words, if you didn’t eat carrots for three years and sporadically ate carrots one day, your microbiome would activate bacteria that was previously dormant to digest the carrots within days. Think for a moment: a bacteria your body hadn’t made in three years is suddenly recolonized and active in helping you digest within a few days. It’s truly amazing! However, the rest depends on how you were born.

If you were vaginally born, your first encounter with bacteria (bacteria from the placenta is still controversial as to whether babies acquire some of their intestinal bacteria before birth) was in the birth canal, which is exactly where you get your microbiota colonies from. If you were Cesarean born, you might find that you have a higher chance of chronic conditions like asthma or Celiac’s disease simply because you received your mother’s skin microbiome instead of her vaginal microbiome. If you were not breast fed, you are more likely to contract similar conditions because breast milk contains nutrients that cannot be broken down by your digestive track. Rather, they surpass your digestive track and nourish microbiota. Formulas were unaware of this and therefore did not contain everything necessary for your microbiota health, but formulas have been making adaptions to fully mimic these qualities of breast milk.

Say you did all of the right things: you eat whole, unprocessed foods that can nourish your microbiome, you were vaginally born and you were breastfed. It’s completely possible that you have a wonderful, flourishing microbiome. However, you likely do not.  Processed foods do not contain enough prebiotic nutrients (food for microbes). Although one associates Western civilization with nutrition and health, we are actually considered “impoverished” in the world of microbiomes.

The big problem with the Western diet is that it doesn’t feed the gut, only the upper G I. All the food has been processed to be readily absorbed, leaving nothing for the lower G I. But it turns out that one of the keys to health is fermentation in the large intestine. Stephen O’Keefe

Those with no contact to the Western world and its medicine, pesticides, sterility and processed foods have a rich and diverse microbiome. Not to mention the growth hormone in cows, which changes the microbiota for a hastened growth as well as the metabolism of the liver. They even stimulate an increase in body fat. Western medicine, however, affects us in less visible manner. Our antibiotics are too strong for our own good; they destroy the pathogenic bacteria, yes, but they also destroy the health-promoting ones. Therefore, some argue that we should improve our diagnostics to prescribe fewer and narrow-spectrum antibiotics to kill the harmful bacteria while reducing the collateral damage. (Dr. Blaser) These heavy duty antibiotics not only destroy the healthy, diverse microbiota, but have a permanent effect if used for a second course; the microbiome will bounce back but it will not be able to return to its original state. In addition to this, antibiotics have been trying to eliminate H. pylori since 1983 when they found it could lead to stomach cancer or peptic ulcers, when in fact its disappearance could be contributing to acid reflux and obesity. Due to our continual efforts to eliminate H. pylori from the microbiome, it is unlikely that we will see it in upcoming microbiomes due to antibiotics, and “each generation is [already] passing on fewer of this microbes.” Prevotella, for example, is a gut bacteria extremely difficult to find in Western society but relatively common in underdeveloped countries. One woman had unusually high levels of this bacteria in her microbiome, but after one course of antibiotics for oral surgery, her wonderful microbiome was reduced to the average American bacterial standards. 

One of the more striking results from the sequencing of my microbiome was the impact of a single course of antibiotics on my gut community. My dentist had put me on a course of Amoxicillin as a precaution before oral surgery. (Without prophylactic antibiotics, of course, surgery would be considerably more dangerous.) Within a week, my impressively non-Western “alpha diversity” — a measure of the microbial diversity in my gut — had plummeted and come to look very much like the American average. My (possibly) healthy levels of prevotella had also disappeared, to be replaced by a spike in bacteroides (much more common in the West) and an alarming bloom of proteobacteria, a phylum that includes a great many weedy and pathogenic characters, including E. coli and salmonella. What had appeared to be a pretty healthy, diversified gut was now raising expressions of concern among the microbiologists who looked at my data.

Her bacterial composition will return to something that somewhat resembles her original microbiome, but every course after that will decrease potential microbial recovery and also decrease invasion resistance (keeps pathogens from gaining a toehold by occupying potential niches or otherwise rendering the environment inhospitable to foreigners e.g. H. pylori regulates stomach acid to make the environment unfavorable to other bacteria that wants to colonize; vaginal pH is kept low so the environment is too acidic for foreign bacteria to colonize, etc.) So the next time you take an antibiotic, ask yourself: what am I doing to my microbiome?

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