BioQuakes

AP Biology class blog for discussing current research in Biology

Tag: gut

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.

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.

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

 

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

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.

 

Have No Fear, Gut Microbes Are Here!

Ever dream about being a real life Captain America? Well, with the help of microbes, we are one step closer to achieving a “super soldier.” Microbes might not make a soldier muscular, but they can help with soldiers’ health and versatility. Scientist Jeff Tabor is working on engineering a probiotic organism that can help humans easily fight diseases, prevent obesity, and change their body’s ability to adapt to certain environments.

The gut bacteria affects many functions of the human body. The digestive system, immune system, and nervous system are all influenced by gut bacteria. Disrupting these microorganisms can cause indigestion, a weak immune system, depression, insomnia, and affect other cognitive abilities. Tabor’s goal is simply to create a microbe that can be consumed to prevent these problems.

Gut Microbe

Gut Microbe

Initially, Tabor wanted to use these microbes to target obesity because scientists have abundant knowledge of obesity at the molecular level. He recently succeeded in genetically modifying E.Coli to detect chemicals in the body that carry disease in mice guts. He hopes to use this modified E.Coli to sense chemicals in the gut that are connected to obesity and then use other molecules to prevent this obesity. The creation of a microbe that can control weight can be extremely helpful for the U.S. armed forces. For example, soldiers going from sea level to the top of a mountain way above sea level experience changes in temperature and pressure. Using this engineered gut microbe, the soldiers can put on weight to help them keep warm on top of the mountain and then lose weight to keep cool at sea level.

Another military benefit that these microbes can provide is to help soldiers operate effectively on little to no sleep or to help soldiers adapt to changes in their circadian rhythms, either from time change or going below sea level in a submarine. Scientists are interested in experimenting with the gut microbe to be able to achieve these goals in the future.

Some people might be afraid of the possible affects that these genetically modified bacteria might have on the human body. However, Tabor’s goal is for the bacteria to stay in the gut for about six hours to do its job and then self-destruct or die naturally to prevent the bacteria for staying in the body too long. There are other concerning issues about creating a microbe that can help prevent obesity. The creation would take away any incentive for humans to eat healthy and focus on their diets because they could just use the microbe to prevent gaining weight. Any new scientific experiment comes with its pros and cons, but using gut microbes for human health, especially for the military, can be a big step in the right direction.

Source Article

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?

Big Brains Come at a Cost?

Having a big brain can be great. Whipping your friends at trivial pursuit, acing every test you take, and flaunting your vast knowledge to the world. But what is the cost? Researchers recently reported in Current Biology on tests run on guppies

flikr
photo credits to iosonoadry

and discovered some evolutionary setbacks to large-brained guppies.

Through tests with large-brained and small-brained guppies, the scientists determined that a large brain can have adverse effects on gut size and reproductive output.

The reason behind this, and the reason why this is important for humans as well, is because of the amount of mass the brain has versus the amount of energy it requires. In humans, the brain accounts for only 2 percent of the total body mass but makes up 20 percent of the energy requirement of the body. As Niclas Kolm said  “It is a remarkably costly organ energetically.” The idea is that there is a tradeoff between the brain and other organs, and as the brain gets bigger and requires more energy, the other organs must get smaller.

The group’s research suggest that humans and primates, animals with large brains, have relatively small family size because of the tradeoff between brain size and reproduction ability.

Thoughts?

http://www.biologynews.net/archives/2013/01/03/big_brains_are_pricey_guppy_study_shows.html

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