BioQuakes

AP Biology class blog for discussing current research in Biology

Tag: human gut microbiome

The Common Misconception Around Antibiotics & New Findings

Gfp-medicine-container-and-medicine-tabletAntibiotics as a treatment are never fun – not only are you most likely dealing with a bacterial infection, but you need to take them on a strict cycle and can be quite aggressive on your stomach. I once had to go on antibiotics for treating a sinus infection, and it didn’t quite make me feel better after taking it. So after, I went on the same antibiotic, Cefuroxime, and took a higher dose, but I was not consistent in taking it and started feeling ill. This reaction was due to the antibiotics impact on the protective bacteria in my stomach’s microbiome. I soon learned more about the effects the antibiotics had on my stomach’s microbiome, and realized the common misconception around antibiotics – that they only benefit one’s health – and how some of the symbiotic relationships with bacteria in there are essential to digestion and immune protection. 

Biological overview

Antibiotics have been around since 1928 and help save millions of lives each year. Once antibiotics were introduced to treat infections that were to previously kill patients, the average human life expectancy jumped by eight years. Antibiotics are used to treat against a wide variety of bacterial infections, and are considered a wonder of modern medicine. However, they can harm the helpful bacteria that live in our gut.

The word antibiotic means “against life”, and they work just like that – antibiotics keep bacterial cells from copying themselves and reproducing. They are designed to target bacterial infections within (or on) the body. They do this through inhibiting the various essential processes we learned in Unit 1 about a bacterial cell: RNA/DNA synthesis, cell wall synthesis, and protein synthesis. Some antibiotics are highly specialized to be effective against certain bacteria, while others, known as broad-spectrum antibiotics, can attack a wide range of bacteria, including ones that are beneficial to us. Conversely, narrow spectrum antibiotics only impact specific microbes.

Antibiotic resistance mechanisms

The Human stomach is home to a diverse and intricate community of different microbial species- these include many viruses, bacteria, and even fungi. They are collectively referred to as the gut microbiome, and they affect our body from birth and throughout life by controlling the digestion of food, immune system, central nervous system, and other bodily processes. There are trillions of bacterial cells made of up about 1,000 different species of bacteria, each playing a different role in our bodies. It would be very difficult to live without this microbiome – they break down fiber to help produce short-chain fatty acids, which are good for gut health – they also help in controlling how our bodies respond to infection. Many antibiotics are known to inhibit the growth of a wide range of pathogenic bacteria. So, when the gut microbiome is interfered with using similar antibiotics, there is a high chance that the healthy and supportive microbes in our stomachs are targeted as well. Common side effects of collateral damage caused by antibiotics can be gastrointestinal problems or long-term health problems (such as metabolic, allergic, or immunological diseases). There is a lot of new research on the gut microbiome, some even suggesting that it impacts brain health by influencing the central nervous system. It is essential that we know more about how we can optimize its overall well-being.

New Research

Tackling the Collateral Damage to Our Health From Antibiotics

Researchers from the Maier lab EMBL Heidelberg at the University of Tübingen have substantially improved our understanding of antibiotics’ effects on gut microbiomes. They have analyzed the effects of 144 antibiotics on our most common gut microbes. The researchers determined how a given antibiotic would affect 27 different bacterial strains; they performed studies on more than 800 antibiotics.

The studies revealed that tetracyclines and macrolides – two commonly used antibiotic families – led to bacterial cell death, rather than just inhibiting reproduction. These antibiotic classes were considered to have bactericidal effects – meaning that it kills bacteria rather than just inhibiting their reproduction. The assumption that most antibiotics had only bacteriostatic effects was proven not to be true; about half of the gut microbes were killed upon being treated with several antibiotics, whereas the rest were just inhibited in their reproduction. 

These results expanded existing datasets on antibiotic spectra in gut bacterial species by 75%. When certain bacteria in the gut are dead, and others are not, there can exist an reduction of microflora diversity in the microbiota composition; this concept is referred to as dysbiosis. This can result in diarrhea, or even long term consequences such as food allergies or asthma. Luckily, the Researchers at EMBL Heidelberg have suggested a new approach to mitigating the adverse effects of antibiotics on the gut microbiome. They found that it would be possible to add a particular non-antibiotic drug to mask the negative effects the antibiotics had. The Researchers used a combination of antibiotic and non-antibiotic drug on a mouse and found that it mitigated the loss of particular gut microflora in the mouse gut. When in combination with several non-antibiotic drugs, the gut microbes could be saved. Additionally, they found that the combination used to rescue the microbes did not compromise the efficacy of the antibiotic.

It has been known for a while that antibiotics were impactful on gut microbiome, but its true extent had not been studied much until recently.  More time is needed to identify the optimal dosing and combinations, but the research coming from the Maier lab is very substantial as it fills in “major gaps in our understanding of which type of antibiotic affects which types of bacteria, and in what way,” said Nassos Typas, Senior Scientist at EMBL Heidelberg.

The Importance of Gut Health: How to Live Long and Be Happy

Gut health – why is it so important? I had always thought that the concept of good gut health was a myth and only lived on the side of a bottle of Kombucha. I could not have been more incorrect!Kombucha, Health-Ade,

It turns out that a happy gut is critical to live a long, happy, and healthy life! The gut, also known as the digestive tract or gastrointestinal track, includes the mouth, esophagus, stomach, small intestine, pancreas, liver, gallbladder, colon, and rectum. Therefore, it processes all of the nutrients you take in, fights diseases, serves as a center for communication, and produces hormones. These are all critical tasks that affect your everyday well-being!

202004 Gut microbiota

When thinking about gut health, scientists are usually referring to the gut microbiome. In short, the gut microbiome is all of the microbiomes in your intestines. Humans would have a very hard time surviving without the gut microbiome. It digests breast milk when babies are first born, controls the immune system, digests fiber, and even helps control brain health. In fact, a recent study done with mice suggests that gut health affects social interaction/behaviors, stress, anxiety, and autism spectrum disorder. Additionally, in 2011 another study was done with mice, which involved antibiotics killing “bad” gut bacteria, also known as, gut flora. These mice became scientifically less anxious after killing the gut flora and “showed [positive] changes in their brain chemistry that have been linked to depression”  according to Live Science.

Gut flora is not the same for everyone. Another study done with gut flora showed that obese individuals tend to have less diversity in their gut flora when compared to lean individuals. This difference is because of an increase in Firmicutes and decrease of Bacteroidetes in obese individuals. Gut flora also affects an individual’s metabolism because of its affects on the breakdown of a key organic compound we have learned about in biology, carbohydrates. As we know, carbohydrates provide energy for the body which is imperative for all individuals. Another subject we have discussed in our class, amino acids, can have an increase in production because of gut flora (Live Science).

Now, you may be wondering, “how can I keep my gut happy?” The key to a healthy gut comes from diet. After an extensive amount of research, here are some tips I have gathered and why they work:

  1. Eat a variety of foods – to keep your microbiome diverse (recommended to eat specifically a variety of fruits and vegetables for fiber, vitamins, and minerals)
    Fresh fruits and vegetables in 2020 06
  2. Eat fermented foods (ex. yogurt, kefir, kimchi, pickles, sauerkraut) – it “can reduce the amount of disease-causing species in the gut” (Healthline)Vegan yogurt, March 2012
  3. Eat nuts, seeds, and legumes for fiber and proteinNuts on Spice Bazaar in Istanbul 01
  4. Eat whole grains for dietary fiberHome made whole grain bread
  5. Eat prebiotic foods (ex. bananas, artichokes, apples, asparagus, oats, flax seeds, garlic, onions, broccoli) – to “help boost the population and diversity of good bacteria” (Orlando Health)29 Nov 2011 - Apples and BananasThree Onion in Peng Chau
  6. Limit antibiotics – they kill both good and bad bacteria in the gut, which decreases necessary varietyAntibiotic pills
  7. Take a probiotic supplement – it “can help restore the gut to a healthy state after dysbiosis” (Healthline)Red and blue pill

These are all relatively small changes for the huge benefits that they reap. Start incorporating them today to improve your gut health and live a longer, happier, and overall healthier life!

 

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?

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.

Your favorite muscular tube,
Jessophagus

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.

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.)

 

Baboons: A closer insight to understanding the Human Gut Microbiome

In a recent Northwestern University article, a new study was found that despite human’s close genetic relationship to apes, the human gut microbiome is more closely related to that of “Old World” monkeys, such as baboons than to that of apes like chimpanzees. Another article posted by Medical News Today, provided more insight on why we should specifically take a deeper look into Old world monkeys, such as baboons, to tell us more about the human microbiome. Maria Cohut, the author of the article, claims that since these baboons are closer related to humans and share 99% of their DNA with humans, they will provide clues about the human gut microbiome. 

The results also suggested that human ecology has had a stronger impact in shaping the human gut microbiome than genetic relationships. They also suggest the human gut microbiome may have unique characteristics, like an increased flexibility. In a quote by Katherine Amato,  lead author of the study and assistant professor of anthropology in the Weinberg College of Arts and Sciences at Northwestern, she explains that it is essential to understand what factors shaped the human gut microbiome over evolutionary time because it can help us understand how gut microbes may have influenced adaptation and evolution in our ancestors and how they interact with our biology and health today. She also adds that host ecology is what drives microbiome function and composition, since chimpanzees have different habitats, diets, and physiology than humans. In order to understand the human gut microbiome we must look at primates that are similar to humans since ecology is the, she also adds. Although chimpanzees are often assumed to be the best module for humans in many aspects, it is evident that this close relationship doesn’t apply when comes to analyzing the gut microbiome. 

Going forward, Amato and her team are planning on exploring which qualities of the human gut microbial functions are shared with Old World monkeys and what impact they have on human biology and physiology. The results of this study demonstrate that the human gut microbiome diverges from closely genetically related apes and converges with “cercopithecines both taxonomically and functionally.” These findings provides deep insight on the evolution of microbiomes. More importantly, the results highlight the importance of human ecology and digestive physiology in shaping the gut microbiome. Intimately exploring the relationship between baboons, or other close human related mammals, could reveal more in-depth information about the human gut microbiome and how different factors of our environment affect it. 

Valuable Poop

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

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

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

Look at that C. difficile, bad stuff!

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

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

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

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

 

Would you get a fecal transplant if it were recommended?

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

What do you think regarding the future of antibiotics?

C. Difficile Colitis: How To Prevent It

What is Clostridioides difficile Colitis, or C. difficile Colitis, and how can you get it? C. difficile Colitis is an infection of the Colon caused by an excess amount of the Clostridioides difficile bacterium in your intestines. Some symptoms of the infection include diarrhea, stomach pain, nausea, vomiting, fever, and blood in stool. C. difficile Colitis is spread by feces, it usually comes from touching a contaminated surface, then touching your mouth. As repulsive as it sounds, it’s actually a lot more common than you might think. Statistics reported by the U.S Centers for Disease Control and Prevention estimated that in 2015, more than 148 out of every 1,000 people contracted C. Difficile Colitis.

Clostridium Difficile Bacteria

 

Experiment:

Confused and concerned by these findings, Kashyap, a Gastroenterologist at the Mayo Clinic in Rochester, Minnesota, alongside her team, decided to conduct an experiment on mice to get to the bottom of this infection. It is known that a disturbance in the combination of gut microbes within a mouse, can, in many cases, cause a C. Difficile infection inside of them. That being said, the researchers, at random, extracted and transported fecal matter from people’s colons with either normal or disturbed microbiomes, and transplanted the gut microbes into the mice’s stomachs.

Results of the experiment, as they predicted, showed that the mice that received transplants from people with disturbed microbiomes were not able to fight off the C. Difficile infection as well as the mice who received transplants from people with normal microbiomes, could. The results showed that, anteceding the experiment, the mice who had received the transplant of disturbed gut microbiomes, experienced an increase in a few specific amino acids found in their gut, especially proline. Proline is a major food source of C. Difficile bacteria, which in turn, strengthens the bacteria, giving it an advantage over other microbes found in the gut, that do not consume proline. This proved that proline-deficient people have much less C. Difficile bacteria in their intestines, thus making them far less susceptible to contracting the infection.

All that being said, the best way to prevent C. Difficile Colitis, is to avoid any and all antibiotics containing proline and to consider taking probiotics with proline-eating bacteria in order to hopefully outrun and weaken C. Difficile bacteria within the intestines, helping to restore the balance of microbes. Please don’t hesitate to comment what you think!

A Possible Way to Prevent Asthma in Infants

Did you know that asthma in infant boys may soon be able to be prevented? Infant boys whose mother’s have asthma are at a higher risk of developing asthma due to genetics. However, according to a study published by the University of Alberta in Canada, the structure of the gut microbiome may also play a role in the development of asthma in these boys. Microbiomes are the bacteria that live in human digestive tracts. The research team, led by epidemiologist Anita Kozyrskyj, studied the characteristics of the gut microbiome in 1000 infant boys born to mothers with asthma.

The team discovered that these boys were one-third as likely to have certain characteristics in their gut microbiome when they were 3-4 months old. The boys had a significantly less amount of Lactobacillus microbes. This evidence suggests that maternal asthma can be associated with the lack of Lactobacillus. The team believes that this discovery could lead to modifying the gut microbiome in these infants to reduce their risk of developing asthma.

The team started this research because they wanted to study the sex-based differences between boys and girls born to mothers with asthma. The gut bacteria on infant girls was affected differently. Girls have more bacteria than boys that maintain a mucus barrier and protect the gut cells. The team believes that this barrier protects the girls from developing asthma as babies, but are more prone to developing it during puberty.

Asthma is a breathing disease that affects many people. It is interesting to learn about how this sometimes deadly disease may be able to be prevented in infants. Although there it is not definite that this can be prevented, it is fascinating to read about this possibility. For more information on gut microbiomes, click here and here. Based on this research, do you think that scientists will be able to find a way to modify the gut bacteria?

 

Could A Computer Detect Your Sick Gut?

Photo by Nicola Fawcett (photo source)

 

The human gut microbiome is a system specially revolved around the genetic makeup of an individual person. These gut biomes are the subject of many studies by scientists who are interested in the small world of bacteria living inside of our stomachs and its relation to our health or illness. Many humans have the ability to recognize a healthy or unhealthy human gut microbiome, however, is it possible for a computer to have this same ability? According to the impressive research results developed by a group of scientists at the University of California San Diego, it is possible for a computer to be trained to differentiate a sick gut microbiome compared to an unhealthy one.

In order to reach this innovative conclusion, these scientists utilized metagenomics, a gene sequencing technique, to break up the DNA of hundreds of microbes residing in the human gut. The scientists took gut bacterial samples from the stool samples of thirty “healthy” and thirty “unhealthy” people. The unhealthy people whom had samples taken from them were either diagnosed with autoimmune Inflammatory Bowel Disease. With these 60 samples total, the scientists were able to sequence 600 billion DNA bases and put the information into a computer. After that, the scientists underwent a complex process of translating reconstructed DNA of the hundreds of microbes into thousands of proteins, which were then categorized into thousands of protein families. The tedious differentiation and categorization of certain proteins allows the scientists to see the activity of the bacteria and then program it into the computer so it, too, would be able to recognize these proteins and bacteria. Bryn C. Taylor, One of the scientists involved in this research says that, “You can try to categorize healthy and sick people by looking at their intestinal bacterial composition…but the differences are not always clear. Instead, when we categorize by the bacterial protein family levels, we see a distinct difference between healthy and sick people.” Incorporating this method of distinction with the storage of healthy and unhealthy patient data into computers is an effective way of “training” a computer how to detect a sick or healthy human gut due to a distinguishable difference in bacterial activity, protein presence, etc..

Overall, it seems that these scientists at the University of California San Diego have made groundbreaking progress in the future usage of computers in the detection of an unhealthy or sick human gut microbiome. Do you think the development of a computer’s ability to detect a sick gut will be ultimately more beneficial to the world of health and science, or will it just be an unnecessary new trick that computers can learn? The next time you feel like you’ve got a stomach bug, you just might be scheduling an appointment with a computer instead of your doctor.

https://commons.wikimedia.org/wiki/File:Wild_garden_of_the_gut_bacteria_3.jpg

 

Parents Take Warning: Antibiotics Can Be Harmful to Infants

Antibiotics are the marvel of modern medicine. They have brought about incredible medical advances, treating bacterial diseases and helping to prolong lifespans in modern times. But a new study conducted by researchers at the Massachusetts General Hospital and the Broad Institute has shined a light on the potential negative effects antibiotics can have on an infant’s health.

https://www.flickr.com/photos/herebedragons/2573487530

The study, conducted in partnership with a team of Finnish researchers, took monthly fecal samples from 39 children from birth until they were 36 months old and analyzed the sample using standard, RNA sequencing procedure to identify different microbes. During the study, 20 of the children had taken antibiotics for respiratory or ear infections ranging from 9 to 15 treatments over the course of the study. From this data, the researchers could analyze the diversity of the gut microbiome of these participants with respect to their antibiotic usage.

The researchers had chosen to analyze the effect antibiotics have on the gut microbiome in young children because of the pivotal role antibiotics appear to play in human health during early development. Low diversity in the early years of life of this collection of bacteria residing in the intestines has been linked to allergies and autoimmune diseases.

The results of this study show a decrease in the diversity of the microbial gut populations in infants who took antibiotics. This was even more pronounced when the infants were marked with a specific signature low in a bacteria known as Bacteriodes (this decrease in Bacteriodes has been speculated to be linked to Caesarean section births in the past but the researchers found this rationale to be inconclusive as well as another rationale that prolonged breastfeeding led to a stronger gut microbiome with higher levels of Bifidobacteria).

When the infants had taken antibiotics, a single strain of bacteria tended to rule their gut with only a few species surviving. On the whole, the gut microbiomes of these participants were less stable and had higher levels of antibiotic resistant genes.

Don’t get me wrong: antibiotics are an incredible innovation that has saved millions of lives. But, be careful in thinking they are a cure all. They’re side-effects might be more harmful than you think, especially in children.

How does this research change your perception of antibiotics?

 

No More Lactase Pills?!

Love milk, yogurt, pizza, and other irresistible dairy products?  Hate having to take lactase pills or face suffering in the bathroom every time after you eat or drink them?  You’re not alone. In fact, it is estimated that around 75% of the entire human population has difficulty absorbing lactose, or the sugar found in milk and dairy products. However, a recent revelation has suggested a way to manipulate the human gut microbiome and circumvent this issue.

Bifidobacteria in human gut microbiome

In a study conducted by Dr. Andrea Azcarate-Peril, an Assistant Professor of Medicine in the School of Medicine at UNC Chapel Hill, it was shown that highly purified (>95%) galactooligosaccharides could indeed improve or often eliminate the indigestion (nausea, cramps, bloating, etc.) felt by lactose-intolerant subjects. To investigate this finding, Azcarate-Peril and her team conducted the following experimentation.

Human subjects were administered the high-purity short-chain GOS, designated as “RP-G28”, and stool samples were collected at three separate times: pretreatment (day 0), post-treatment (day 36), and after the GOS feeding was halted and the subject was encouraged to consume dairy products (day 66).  To analyze changes within the fecal microbiome, scientists used 16s rRNA amplicon pyrosequencing and high-throughput quantitative PCR.  Samples from day 36 saw an increase in bifidobacterial populations in 27 out of the 30 subjects (90%).  This confirmed that GOS resulted in a bifidogenic response in vivo.  Additionally,  GOS induced a significant increase in the relative amount of lactose-fermenting Facecalibacterium and Lactobacillus.  Then, when dairy was introduced into the subjects’ diets (day 36 to day 66), lactose-fermenting Roseburia species presence increased.  In conclusion, the results of Azcarate-Peril’s work indicate that a GOS diet can cause a definitive change in the fecal microbiome of a lactose-intolerant individual, increasing concentrations of a lactose-metabolizing bacteria.  The change discovered has been correlated with improved lactose tolerance in patients at the clinical level.

We might be on the verge of helping millions upon millions of people who are lactose malabsorbers!  As an individual who struggles with lactose intolerance, this is fantastic news and I cannot wait for more research to be conducted in this domain.  What other gastrointestinal issues could we solve by affecting the human gut microbiome?  Are we on the road to curing inflammatory bowl disease (primarily ulcerative colitis and Crohn’s disease)?

 

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.

 

New Discoveries Link Stomach Bacteria with Autism

Autism rates are on the rise in the US, and the cause of this condition is still unknown.  Autism is mental condition, present from early childhood, characterized by difficulty in communicating and forming relationships with other people and in using language and abstract concepts.  According to the CDC, 1 in 68 children will be born with autism.  This is a huge increase from the 1 in 150 children in 2000.  It is unknown how autism starts, but something causes a change in brain structure or function that leads to the condition.  New research shows that it could possibly be related to the human gut microbiome.

Mycobacterium tuberculosis Bacteria, the Cause of TB

Image Source

Since the 1990’s, the gut microbiome has been the topic of copious amounts of research.  Scientific developments since then have uncovered the influence that the gut microbiome has on human health.  Disorders in the microbiome have been linked to conditions like asthma, rheumatoid arthritis and even some cancers.  New research claims that over representation of Clostridium or Desulfovibrio bacteria in the microbiome could possibly cause the autism spectrum disorders.  According to the report, “Studies of fecal DNA extracts have found Clostridium or Desulfovibrio clusters over-represented in children with gastrointestinal complaints and ASD(autism spectrum disorders) as compared to children with similar GI complaints but typical neuro-behavioral development”.  A another possible link between the microbiome and autism was found when clinical improvement was reported in children with autism who developed fever, received antibiotics, or ingested probiotics— treatments that likely altered gut bacteria, thus limiting the effects of the bacteria. 

While the connections may be weak right now, discovering potential connections between autism and the gut microbiome allows for more research and a potential cure one day.  One researcher plans on conducting a clinical study using fecal transplants from healthy donors. The goal of this study is to see if the treatment “would reduce autism symptoms by normalizing an individual’s community of gut bacteria.”

Original Article

Further Reading:

https://www.autismspeaks.org/science/science-news/autism-study-more-evidence-linking-altered-gut-bacteria-asd

 

It’s Time to Re-program the Human Gut

(Photo of the human gut (licensing information here)

“What kind of water would you like? Tap or bottled?” “Bottled, please.”

It is known that when traveling internationally, it is typically unsafe to drink tap water. This is due to the lack of familiarity with the filtering systems used by other countries. This caution extends to certain foods as well. However, Dr. Pamela Silver, Dr. Jeffrey Way, and Dr. Donald Ingber, investigators at Harvard’s Wyss Institute for Biologically Inspired Engineering, may have found a solution to many acute gastrointestinal illnesses, such as this one, that affect the human gut microbiome.

Their goal is to create a bacteria that can detect and fight microbial invaders. This genetically engineered bacteria will specialize in detecting the chemicals given off by gastrointestinal inflammation. After the bacteria makes the detection, it will begin to attack all microbial invaders and restore normality within the gastrointestinal tract. The bacteria will be created in a probiotic pill form. In order to make sure that this probiotic pill does not have a negative impact on the environment after it exits the gastrointestinal tract, Silver and Way will ensure that it will not work unless it is in a specific environment and is triggered by specific chemical signals, both specific to the environment and signals found in the gastrointestinal tract.

Silver, Way, and Ingber will use the gut-on-a-chip technology to test this probiotic pill. The gut-on-a-chip technology will allow them to mimic gastrointestinal inflammation with living human cells. The team plans to study the response of invaders and pathogens, that are causing the inflammation, to the genetically engineered bacteria.

This research will allow for the treatment of a multitude of gastrointestinal illnesses, as well as the introduction to treating other diseases that negatively impact the human gut microbiome. I would love not having to worry about what I drink or eat on vacation! I am excited to see where this newly found research takes the discussion and the treatment of illnesses related to the human gut micobiome.

Source: Biology News

Bringing the Human Gut Microbiome into the Light

The human gut microbiome is an incredible system of symbiotic organisms. These micro-organisms that provide us with vitamins and amino acids as well as break down toxins and protect us from harmful invaders. We could not live without them and they could not survive without their host, us. We carry over 3 pounds of these little helpers in our body and outnumber our cells. Although this system is so important to our survival, it has been hard to study for long periods of time, until now. Judah Folkman, professor of Vascular Biology at Harvard Medical School states, “”Until now, use of traditional culture methods and even more sophisticated organoid cultures have prevented the microbiome from being studied beyond one or two days. With our human gut-on-a-chip, we can not only culture the normal gut microbiome for extended times.”

 Escherichia coli

E. Coli 10000x magnified

https://en.wikipedia.org/wiki/Fecal_bacteriotherapy

The human gut-on-a-chip is constructed from a clear, flexible polymer roughly the size of the a flash drive. This chip simulates the environment of our gut so well that cultures can last up to weeks. This extended period of time can allow for major breakthroughs in the study of the microbiome and what happens when things do not go as planned. Judah Folkman adds, “we can also analyze contributions of pathogens, immune cells, and vascular and lymphatic endothelium, as well as model specific diseases to understand complex pathophysiological responses of the intestinal tract.”

 

The Wyss team thinks that this new technology can help treat patients by eventually culturing there own cells and microbiome on the human gut-on-a-chip to test different treatments. This new technology, although not directly discovering anything about the human gut microbiome, will lead to major discoveries down the line.

 

Main Article:

http://www.sciencedaily.com/releases/2015/12/151214165918.htm

 

Other Articles:

http://www.sciencedaily.com/releases/2014/07/140707103641.htm

http://www.britannica.com/science/human-microbiome

https://en.wikipedia.org/wiki/Human_Microbiome_Project

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.

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