BioQuakes

AP Biology class blog for discussing current research in Biology

Category: Student Post (Page 1 of 48)

Discovering and Using Your Personal, Biological, Tiny Army

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

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

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

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

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

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

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

Is it Time For a Raw Food Diet?

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

 

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

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

The Making of the Largest Human Microbiome Database

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

 

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

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

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

 

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

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.

 

Health and Disease in a New Light

Microbiota are groups of organisms that live on and in some mammals. Animals, such as humans, who live in a state of mutualism with these organisms have them mostly on parts of their body with large surface areas. This includes skin and the intestinal tract. The human gut microbiome is a complex community of organisms that have been studied over the past decades and most intensely within the past fifteen years. So far the information on the human gut microbiome is limited and the research on it is somewhat inconclusive, raising more questions than it answers questions; however, that is a side effect of most research that is just beginning to be analyzed more in depth. The idea that we are just now starting to study and understand these organisms that have lived on and in us for centuries is a topic that is cutting edge and very interesting.

Microbiota

A short coverage of information about microbiota in the intestinal tract includes the following. In mammalian animals, these organisms play an important role in the formation of intestinal mucosa as well as a healthy systematic immune system. Animals that lack microbial cells contain abnormal numbers of several immune cell types and immune cell products, as well as have deficits in local and systemic lymphoid structures. Therefore, their spleens and lymph nodes in them are poorly formed and their intestinal mucosa, deficient. Mice with a lack of microbiota were known to have a lower amount of plasma producing cells – which make antibodies of a certain type. This is due to the fact that the microbiota is regulated by the plasma cells in mammals and it is found unnecessary to have a large amount of them in animals lacking the organisms. These mice also exhibited an impaired ability to regulate cytokine levels – any of a number of substances, such as interferon, interleukin, and growth factors, which are secreted by certain cells of the immune system.

In 2010 there was a study done that was comprised of making cultures of these organisms and bacteria in the human intestinal tract outside of the human body because we do not have the necessary technology to study the microbiota in their hosts. This study yielded the publication of a paper titled “Gut Microbiota in Health and Disease” which gives a detailed overview of the findings of this study. Briefly, a colonization of mice lacking microbiota with altered Schaedler flora (ASF) was insufficient to promote differentiation of Th17 cells (which play an important role in defense against infection), despite the fact that ASF includes a number of bacteria from the Bacteroidetes phylum (microbiota). Researchers concluded the there is no way to be sure of the affects of microbiota. Meaning although there was no lack of microbiota, the mice still had an immune system deficiency in the same way that mice lacking any microbiota did. Since the health and abundance of microbiota in the gut microbiome is so closely related with the ability of the immune system of the host, it is concluded that changes in the microbiome can lead to onset of diseases/illnesses in the host. These factors can also change with environmental changes such a dietary choices of the host. Understanding the dynamics of the gut microbiome under different conditions will help us diagnose and treat many diseases that are now known to be associated with microbial communities.

Analyzing the affects of microbiota in the human gut can reveal topics about human pathology that we did not know before. Therefore, scientists look forward to the development of studies on this topic.

Who’s Smarter: Girls vs. Boys?

According to the legendary myth, boys are smarter in science, technology, engineering and mathematic fields due to biological deficiencies in math aptitude. Recent studies show that this is not true. A study, by Jessica Cantlon at Carnegie Mellon University, evaluates 104 young children by scanning their brain activity while watching an educational video. When the scans were compared, it showed that both groups were equally engaged while watching the videos and there was no difference in how boys and girls processed math skills. To further this study, researchers compared brain maturity in connection to skill, by using brain scans of adults who watched the same educational video. Which concluded that the brains scans in adults and children -of both genders-  were statistically equivalent. This study confirmed the idea that math activities, in both genders, take place in the intraparietal suclus, which is the area of the brain involved in processing numbers, addition and subtraction, and estimating.

So, why are mathematic and computer science fields predominantly males? Well, it could be for the held stereotype that women and girls are biologically inferior at mathematics. This conventional image could also be linked to the fact that females were prevented from pursuing higher education until the 19th century. To show this unconscious bias, an Implicit Association Test was taken by employers. This test reveals an unconscious bias by forcing you to quickly group various words together. If the word man was immediately linked to math, then an implicit bias is shown. This study unveiled the prejudice that men were twice as likely to be hired for a simple math job since, men and women employers displayed a prejudice against women for a perceived lack of mathematical skill.

Don’t Kill Me Immune System! I’m a Friend.

Believe it or not, but not all bacteria is out to get you, especially some of your gut bacteria. These helpful bacteria can aid in digestion and overall healthy, but the question is, why doesn’t your immune system kill them just like harmful bacteria? In other words, how does the immune system differentiate between good and bad bacteria? For now, we are not really sure, but a study from March of this year by Immunologist Ivaylo Ivanov and his team at Columbia University could bring us closer to understanding this form of cell signaling.

The study focuses particularly on the interaction between T cells and segmented filamentous bacteria in the gut. Normally, the immune system would produce antibodies that would bind to antigens on the foreign cell’s surface. As a result, the cell would be marked for destruction by the immune system. However, through an experiment on mice, the researchers found that although the T cells were activated by the segmented filamentous bacteria, the T cells did not destroy the bacteria.

These gut bacteria located in human, mouse, and fish intestines cling themselves to the gut wall and have antigens. So why aren’t they killed? Well, the antigens are packaged in tiny vesicles located near the tip of the hook-like appendage that the bacteria uses to cling to the gut wall: the holdfast. Sorry, that’s about all I can give you. The rest is speculation at this point.

Nonetheless, Ivanov and his team discovered something previously unnoticed by finding these vesicles that hold antigens in segmented filamentous bacteria. They speculate that the T cells read antigens in different ways based on whether or not it’s exposed on the outside of the cell or packaged in a vesicle. In the end, this a big discovery that peaks my interest, especially for its implications on the study of cell signaling. What’s your hypothesis as to why the T cells don’t attack the gut bacteria?

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

What is Starch?

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

Different Types of Starches

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

How are Resistant Starches Beneficial?

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

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

Common Uses For Resistant Starches

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

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

 

 

 

Can the microbiome influence stem cell growth and effectiveness?

The human microbiome is one of the most overlooked and under appreciated aspects of the human anatomy, mostly because it isn’t technically us. When you think of the microbiome, you instantly think of the stomach. Well, another organ the microbiome can have a large affect on is the large intestine. In my research this summer, I went in depth into how high fat diets can affect cancer and inhibit stem cell growth. Specific fats like arachidonic acid, or any type of lard, can cause stem cells to lyse and become bubble-like structures, instead of the branching structure they are supposed to have. These fats can also cause genetic discrepancies, and cause certain genes like Lgr5, which controls stem cell mitosis, to either be lessened or exponentially greatened, either way it isn’t good.

These stem cells are housed in crypts in the colon, and are surrounded by mainly Paneth cells and enterocytes, and remain dormant in these little holes in the colon until they’re called upon. When they are needed, they are used to repair possible tears in the intestine, or for some other function.

Now, you’re probably wondering what all of this has to do with the microbiome, but that’s what I will now explain. If an unbalanced diet is added to the gastrointestinal tract, it can have a negative effect on the microbiome and cause it to not do its job properly. As I previously stated, this can also inhibit the stem cell growth and reproduction in the colon, and can even cause cancer. Most of the microbiome is found in the small intestine and colon, as stomach acid makes the stomach wall almost completely sterile. Therefore, a poor diet will have the biggest impact on these two organs. If a poor diet is present, this can increase the amount of bad bacteria and parasites found in them. These parasites and bad bacteria can then damage and kill the already compromised stem cells, and can also begin to damage the intestine itself, which then can’t be repaired because of what has been done to the stem cells already.

This goes to show that what we eat can have a much bigger impact throughout our entire bodies than we can possibly imagine, and is a prime example as to why a balanced and healthy diet is necessary.

 

Yes, Some of Us Have Different Human Ecosystems.

Our human ecosystems inside of us are composed of countless quantities of cells. However, only 10% of those cells are human cells.  Jeroen Raes , a Biologist based in Belgium, made a vital and fascinating discovery about the other 90%. He discovered that there are three different possible ecosystems inside individual humans. Each person has one of these three ecosystems: bacteriode, prevotella or ruminococcus. These ecosystems are composed of hundreds of trillions of harmless bacteria. One could explain our relationship with these bacteria as symbiotic, as we give them a share of food and they return the favor by helping us digest food and convert it to energy. Furthermore, these bacteria help us fight disease, and can even make us happier by triggering our neurons to release more serotonin. Raes’ experiment tested people from the US, Japan, and Denmark. Despite each regions unique diets, Raes claims to have found no correlation between diets and their individual ecosystems. Furthermore, Raes found no correlation between their age/genetic makeup and individual ecosystems.

People who have the bacteriode system “have a bias” toward bacteria that get most of their energy from proteins and carbohydrates. Bacteriode ecosystems also have more bacteria that make greater quantities of vitamins C, B2, B5, and H. On the contrary, both prevotella and ruminococcus ecosystems mostly digest proteins that are sugar coated. Both of these ecosystems also have more bacteria that create vitamin B1 and folic acid.

Raes’ findings have yielded very confusing results. Even Raes has conceded that he is unsure as to why only three total human ecosystems exist. Moreover, Raes admits his sample size of only a few hundred people will increase with more time and funding. Raes hopes to further his research on these unique human ecosystems, and potentially find links to obesity, diabetes, Crohn’s disease, and autism.

 

Can Processed Foods Soon Be Harmless?

Any discussion of processed foods usually revolves around the negative effects of consuming them. However, a new study has found a specific human gut bacterial strain called Collinsella intestinalisthat is capable of completely reducing the drawbacks of eating processed foods.

Scientists from Washington University School of Medicine in St. Louis discovered that Collinsella intestinalis breaks down the chemical fructoselysine into pieces that do not affect the host’s body. Fructoselysine is one of the chemicals that are formed during food processing. It is commonly found in numerous processed foods that we eat, such as pasta, chocolate, and cereals. In the study, mice were given samples of Collinsella intestinalis as well as processed foods to see how the human gut bacteria would interact with the fructoselysine.

The primary function of the human gut microbiomes is to “digest food otherwise indigestible by human enzymes and deliver nutrients and metabolites for the biological benefit of the host.”

Results from the study showed that mice with the Collinsella intestinalis in their system showed “an increase in the gut microbial communities’ ability to break down fructoselysine into harmless byproducts.” The fructoselysine was “metabolized more efficiently” in the presence of the Collinsella intestinalis.

One scientist from the study noted that “future studies are required before scientists will be able to identify specific capacities of individual microbes to clean up potentially deleterious chemicals produced during modern food manufacturing.”  Humans aren’t completely immune to processed foods just yet.

However, it is still promising that scientists have found that Collinsella intestinalis is in our foreseeable future in terms of being able to eat processed food without any negative effects. Processed foods are consumed by many people throughout the world, and with this recent study they may not be as harmful as people think.

Microbes Role in Evolution

In the human body, there are trillions of bacteria that come together to make a collective group called microbiomes. These cells are an essential part of the human body and regulate our risks to get obesity, asthma, and allergies. Considering microbials help our bodies function, researchers then are wondering if microbials have played a critical role in our evolution. In an article by Carrie Arnold a writer at Scientific American, she illustrates microbiome’s effect on evolution through two studies on insects.

Microbiome’s Effect on Mate Selection

Eugene Rosenberg of Tel Aviv University conducted an experiment in 2019 which found that raising fruit flies on different diets changed their mate selection. During this experiment, the fruit flies would choose to mate with flies with the same diet as them. The flies would revert back to there original mating patterns after they were given antibiotics. The results showed that the changes in the gut microbes from the diet caused the flies to change their choice of mate.

Microbiome’s Effect on Longevity and Ability to Reproduce

In 2011 Geneticist Seth Borderstein at Vanderbilt University conducted an experiment with two types of termites – Zootermopsis angusticollis and Reticulitermes flavipes – to test an organism’s life span and their ability to make offspring. The study found that after the study the antibiotic fed termites had less of a variety of gut bacteria and fewer offspring. The lead researcher Borderstein then concluded that there were important microbes reduced by the antibiotics. Because microbes help with digestion and the absorption of nutrients this reduction left the termites malnourished thus producing fewer eggs.

Conclusion 

These two studies help to illustrate that researchers can no longer see a separation between an organism’s genes and their microbiomes. They both work together in a single hologenome. One of the researchers, Rosenberg, says that by looking at the history of botany and zoology we can see how billions of microorganisms are connected to most animals and plants. Scientists have to look at hologenome in order to understand an organism. Microbiomes are also important in human evolution too. This is shown through human adaptations of digestion, smell, and the immune system. Borderstein says that these changes over time are very likely to be a product of microbiomes in the body. Bordenstein ultimately argues “the microbiota are as important as genes.”

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? 

 

 

 

Artificial Sweeteners – Not So Sweet Anymore

Could it be that artificial sweeteners speed up the development of the very disorders they were designed to prevent? According to a recent study, the answer is yes. Artificial sweeteners, intended to aid diabetes prevention and weight loss, actually have the opposite effect, adding to the epidemic sweeping the nation.

A study by graduate student Jonathan Suez found that artificial sweeteners directly affect the body’s ability to utilize glucose. In his experiment, mice were given water containing the three most common artificial sweeteners in the same quantities allowed by the FDA. The mice in the study developed a glucose intolerance as compared to those in a control group of mice with regular and sugar water.

The scientists repeated the experiment a second time, changing the types of mice and dosage of artificial sweeteners. Even so, the results were the same- artificial sweeteners induced a glucose intolerance in the mice. But why?

The researchers coined a hypothesis that the sugar substitutes change the function and composition of gut microbiota, or the population of bacteria that reside in the intestine. The body does not recognize the artificial sweeteners as “food,” so they are not absorbed in the digestive tract. Thus, they pass through to encounter the millions of bacteria in the gut microbiota, which are directly responsible for harmful effects on the metabolism.

Fun Gut Microbiota Cartoon Model

This hypothesis was confirmed in a follow-up experiment. Researchers gave mice antibiotics that eliminated the majority of their gut bacteria and then transferred the microbiota from mice that had consumed artificial sweetener to these germ-free mice. The researchers found that the transfer of the harmful microbiota also meant a transmission of the glucose intolerance. Indeed, changes to gut microbiota populations by artificial sweeteners promote glucose intolerance and health complications.

The experiment modeled on mice is also applicable to human beings. Further study and data from the personalized nutrition project, a self-reported program that tracks the relationship between nutrition and microbiota, showed a significant association between artificial sweetener consumption and glucose intolerance by those who shared their responses. Similarly, the researchers conducted a controlled experiment with participants who normally did not consume artificially sweetened foods but ate entirely artificially sweetened products for a week and saw that those in the study began to develop glucose intolerance after only seven days. They also saw a change in the composition of their gut microbiota, discovering two different populations of human gut bacteria – one that induced glucose intolerance when exposed to the sweeteners, and a second that did not affect people either way.

One researcher, Elinav, hypothesizes that the reasoning for this is that certain bacteria in the guts of the affected individuals reacted to the chemical sweeteners by producing substances that cause an inflammatory response similar to that of a sugar overdose. This then changes the body’s ability to utilize sugar and gives rise to diseases, such as those like diabetes discussed earlier.

These findings are worth considering when consuming varying cuisines in day to day life. I know I’ll definitely rethink when I find myself reaching for the “healthier alternative,” considering whether its a reality or merely a marketing technique. How do you balance the consumption of healthy and less favorable meals, treats and snacks, in your daily life? Let me know in the comments below.

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

What is the Human Gut Microbiome?

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

 

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

A Unique Passcode

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

Why Else is the Microbiome important

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

Conclusion

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

The Human Gut Microbiome: Cooperation or Competition within Our Bodies

The human gut microbiome is home to many different types of small bacteria which help the human system function. These intestinal bacteria hold millions of genes that assist with human metabolic function. However, over time scientist have become more interested in the interaction between these bacteria and the human system in regards to diseases that they may prevent through their creation of micronutrients. The most common of these micronutrients are B-vitamins. These B-vitamins specifically, B-1,2,3,5,6,7,9, and 12 are all produced by the bacteria in the human gut microbiome. Along with queuine, these micronutrients allow the gut microbiomes to grow and assist in human bodily functions. In the study lead by Andrei Osterman, the goal was to investigate these microbiomes more and their influence on the human body through their creation of micronutrients.

The scientists on the study’s first objective was to determine the way that the microbiomes created their micronutrients. There are two methods in which the microbiomes can produces these vitamins, de novo or dependent. The ones that produce it de novo mean that they create with own micronutrients through their own process, while the others are dependent on the micronutrients of other microbiomes either older ones or ones close in distance to it. This idea brought about the question as to do the two types of microbiomes compete for these resources or do they coexist. Surprisingly, through research, the scientists discovered that the two types of microbiomes actual peacefully coexist and cooperate in the sharing of the resources. Instead of the dependent microbiomes stealing from the de novo ones, they actually understand the importance of their providers and work with them in return for their micronutrients.

This fact of the peaceful coexistence between the two types of microbiomes then caused Osterman and his team to wonder how the de novo microbiomes are able to distribute the vitamins to both the dependent microbiomes and its human host. To learn more about this process, the researchers looked at the genome of the two different types of microbiomes and marked them separately. The de novo type was given a variant code “P” which stood for prototrophic and the others were given a variant code “A” for auxotrophic. These two codes help them distinguish between the different types of microbiomes and their district pathways. It was discovered that the pathway that the auxotrophic microbiomes used to receive nutrients was called the downstream pathway. This pathway is a flow of vitamins from the phototrophic microbiomes downstream into an area in which the auxotrophic microbiomes can uptake the food.

As the scientists learned more about the pathways in between the different types of microbiomes, they also discovered that some of their original predictions were incorrect. While they believed to have discovered through the phenotype which microbiome was de novo and dependent, with more information on the subject, they began to see the flaw in their original thinking. They discovered that some of the predetermined microbiomes actually were both part de novo and dependent. They had a place to create micronutrients while having downstream pathways to receive it.

Through their research, Osterman and his team were able to discover facts about the way the human gut microbiomes transfer and create nutrients and vitamins to transport to other microbiomes and the human host itself. While very important to our bodies, it is strange to think about the different types of bacteria living in ourselves and their over microbiomes that they have within us. Please feel free to comment your ideas regarding the whole entire world that lives within ourselves in septic our human gut microbiomes.

173 Species of Gut Bacteria Newly Sequenced!

The health of our gut is essential to the everyday function of our body — our gut focuses on the breaking down, transfer and excretion of the food we eat. As such, the balance of bacteria within our gut especially when it comes to breaking down molecules. In particular, the bacteria in the lumen of our colons “ferment the carbohydrates to short chain fatty acids, which are absorbed to provide a second energy source” (Warell, Cox and Firth). Due to the importance of bacteria within the gut, research and advancement in the gut weighs heavily on our ability to interact with problems involving digestion — obesity being a prominent one.

At the Wellcome Trust Sanger Institute, 173 species of bacteria were sequenced for the first time, including 105 species that were isolated for the first time as well. It’s incredible that so many species were identified and isolated for the first time all in one institution. To those who don’t know, DNA sequencing is a process that determines the genetic details of a DNA section: in this case, the DNA sequencing helps scientists determine the genetic information of gut bacteria. This genetic information is highly useful in determining the effects of bacteria — as DNA directly affects the production of proteins, like enzymes in the gut.

While research on the gut relied on mixed-samples of gut bacteria, this new research frees scientists to better identify and isolate each component species. The very foundation of bacteria research has shifted with so many species of bacteria finally open to more specific experimentation, and I’m so excited to see that even the basics of gut research has completely advanced. Not only does this show us the ever-changing advancement of how scientists conduct research and create experiments, but this also holds so much hope for the future: our gut holds importance within our day to day well being, and the ability to conduct much more specific experiments will open up our ability to treat different gastrointestinal disorders.

Can Microbes Create Healthier Food?

A specific human gut microbe is making processed foods healthier. 

Researchers at Washington University School of Medicine in St. Louis wanted to find the chemicals in processed foods that correlate to diabetes and heart disease. In their study, the scientists used a bacteria called Collinsella intestinal (bacteria that contains an enzyme to break down Fructoselysine), which breaks down fructoselysine into small, harmless parts. According to Ashley R. Wolf, a researcher in the lab, “Fructoselysine is common in processed food, including ultra-pasteurized milk, pasta, chocolate and cereals.” This chemical has been linked to the cause of many diseases of aging.

When Wolf and her team tested the effects of feeding fructoselysine to mice that had Collinsella intestinalis, they not only discovered an increase in the amount of microbes in the stomach, but also found that the mice’s gut microbes had a stronger ability to break down fructoselysine.

“The new tools and knowledge gained from this initial study could be used to develop healthier, more nutritious foods as well as design potential strategies to identify and harness certain types of gut bacteria shown to process potentially harmful chemicals into innocuous ones,” says Jeffrey I. Gordon, a researcher of the lab.

Picture of human gut microbes

(“Courtesy of Pacific Northwest National Laboratory”)

Another study by Harvard University and the University of San Francisco, discovered that raw food was healthier than cooked food. They found that “cooked food allows the host to soak up more calories in the small intestine, leaving less for hungry microbes further down the gut; on the other hand, many raw foods contain potent antimicrobial compounds that appear to directly damage certain microbes.”

Although more research still has to be done to determine the effectiveness of the microbe, these discoveries help lead people into a healthier lifestyle. 

How The Animals of Africa Can Help To Understand The Human Body

Scientists have been studying the microbiome of animals and humans for years. DNA analysis has proved to be a method of research that allows scientists to understand the microbiome better. Researchers at Brown University have recently added onto this knowledge by conducting a study focusing on the microbiomes, diets, and environments of animals.

The Study:

In a recent study conducted by Brown University, scientists analyzed animals’ feces collected by researchers in Kenya in order to further explore the relationship between the microbiome, environment, and diet. The had researchers from the Mpala Research Centre in Kenya collect approximately 1,000 samples of feces from 33 different herbivore species such as elephants, giraffes, and antelopes. The samples were then analyzed, specifically the DNA in the samples were analyzed, and the researchers came to three conclusions.

Conclusions:

One, similar or closely related species showed evidence of similar microbiomes. Two, animals with different diets had different microbiomes. Three, animals experienced environmental seasonal changes also experienced seasonal changes in their microbiome. Based on these conclusions, Tyler Kartzinel, a current assistant professor at Brown University and former researcher of Princeton University, hopes to further study the degree to which seasonal changes affect certain animals’ microbiomes and answer questions such as whether or not seasonal sensitivity in the microbiome is a sign of good health.

Why Is This Important?

The findings of this study have opened up a door to more question to be answered and research to be done. Future research will focus on the health of wild animals whose microbiomes change significantly based on their seasonal sensitivity. This is only the beginning of a series of studies that could continue on to figuring out how we can manage the human microbiome in order to improve overall human health using DNA and genetic findings. I think it is very interesting how some samples of animal feces in Kenya could be the start of a series of studies used to improve the health of humans. What do you think?

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.)

 

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