BioQuakes

AP Biology class blog for discussing current research in Biology

Tag: bacteria (Page 1 of 3)

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.

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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.

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.

 

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.

 

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.

Adapted Bacteria vs AI

In a recent article it has been found out by researchers at Washington State University that it is possible to find antibiotic resistant genes in bacteria with machine learning and game theory.

In the world of health and medicine one of, if not the biggest discovery is antibiotics. They were the most simple way of clearing out or slowing down the reproduction of bacteria in the human body. People a long time ago had been dying left and right to bacterial deseases and antibiotics helped the expectancy of everyone’s lives. However eventually after it started being used bacteria with DNA that has antibiotic resistance survived and reproduced. Eventually it could be problematic as there’s many ways to acquire resistances as said here. With certain bacteria that many people used to be infected with a lot and since people used antibiotics for it certain bacteria had vast resistances as there’s very limited antibiotics to kill one type of disease. If there was a strand of bacteria completely used to antibiotics it could wipe out the human race. If you want to learn more on that it could be found here

 

Although it isn’t too bad and we haven’t run into many bacteria that resist antibiotics, it can also be very dangerous if a person takes an antibiotic that the bacteria in their body is resistant to. The bacteria then wouldn’t die and thy would also expand and live on to reproduce and make the problem worse since it was technically not treated. However with what the people in Washington state university are doing computers would more and more be able to find the bacteria that have genes resistant to certain antibiotics.  The AI would learn more and more what genes are likely to be ones that resist antibiotics and they will be able to apply that to other situations. This method used worldwide would really help people know what type of antibiotics to give sick people. If a strain of bacteria is treated with antibiotics that most of it is resistant to not only could the person die but the existing bacteria in that persons body could be extremely dangerous if it reproduces as said before. So knowing if that bacteria does indeed have a resistance could be pivotal in many peoples lives. This could also happen at new speeds since that is one of the biggest advantages of using AI.

Not only is this new method very fast it is also very efficient. The researches at Washington state had been able to determine this at an accuracy rate ranging from 93% -99%. These constant advancements in health and technology show how the implementation of tech into health has changed life as we know it and will continue to forever.

Danger in the Growing Animal Product Industry

As more countries begin to mass produce animal products, more antimicrobials are used to keep the animals from spreading disease. However, this commonplace antimicrobial use results in antimicrobial resistance, specifically in low and middle-income countries with few rules in place. Interestingly, most instances of microbial resistance occur in Asia and South America, but there are few instances in Africa.

Once animals develop antimicrobial resistance, it affects the rest of the food chain. When farmers give their animals antimicrobials, all of their stomach bacteria besides the resistant kind is killed. As a result, antimicrobial-resistant bacteria can spread to the soil, to produce, and to humans. Potentially, in a world without antimicrobials, even simple surgeries can be unimaginably dangerous, and diseases can be difficult to treat. At the moment, in certain countries, people are developing drug-resistant strains of malaria, tuberculosis, influenza, and even HIV.

A description of how drug resistant bacteria reproduce after other bacteria are killed.

Researchers have multiple ways of testing the spread of antimicrobial resistance. They can search for pockets where animals carry illnesses that are resistant to antimicrobials, such as penicillin. Researchers now test how many animals have resistance to drugs by giving them drugs and seeing if the animals respond. In antimicrobial-resistant hotspots, up to 50% of animals may not respond to drugs. People can struggle to find accurate information regarding the amount of drug-resistant animals, specifically in South America, where information is not always public. Researchers have also created the Resistance Bank, where people can see the specific antibiotics animals are resistant to. Its goal is to increase awareness in lower-income countries who may not have the resources to publish scientific articles describing the levels of antimicrobial resistance.

How can we protect ourselves from this growing threat? On a global scale, the spread of antimicrobial-resistant diseases can only be completely slowed with the halting of overuse on people and animals. In contrast, if we each wash our hands often, cook meat before eating it and use separate preparing utensils for raw meat and all other foods, and spread awareness about the overuse of antibiotics, perhaps each one of us can help halt the spread of antimicrobial-resistant infections.

 

New anti-CRISPR Proteins Serving as Impediments to this Miraculous System.

CRISPR-Cas9 systems are bacterial immune systems that specifically target genomic sequences that in turn can enable the bacterium to fight off infecting phages. CRISPR stands for “clusters of regularly interspaced short palindromic repeats” and was  first demonstrated experimentally by Rodolphe Barrangou and a team of researchers at Danisco. Cas9 is a protein enzyme that is capable of cutting strands of DNA, associated with the specialized stretches of CRISPR DNA.

Diagram of the CRISPR prokaryotic antiviral defense mechanism.

Recently, a blockage to the systems was found by researchers which are essentially anti-CRISPR proteins. Before, research on these proteins had only showed that they can be used to reduce errors in certain genome editing. But now, according to Ruben Vazquez Uribe, Postdoc at the Novo Nordisk Foundation Center for Biosustainability (DTU), “We used a different approach that focused on anti-CRISPR functional activity rather than DNA sequence similarity. This approach enabled us to find anti-CRISPRs in bacteria that can’t necessarily be cultured or infected with phages. And the results are really exciting.” These genes were able to be discovered by DNA from four human faecal samples, two soil samples, one cow faecal sample and one pig faecal sample into a bacterial sample. In doing so, cells with anti-CRISPR genes would become resistant to an antibiotic while those without it would simply die. Further studies found 11 DNA fragments that stood against Cas9 and through this, researchers were ultimately able to identify 4 new anti-CRIPRS that “are present in bacteria found in multiple environments, for instance in bacteria living in insects’ gut, seawater and food,”  with each having different traits and properties.  “Today, most researchers using CRISPR-Cas9 have difficulties controlling the system and off-target activity. Therefore, anti-CRISPR systems are very important, because you want to be able to turn your system on and off to test the activity. Therefore, these new proteins could become very useful,” says Morten Sommer, Scientific Director and Professor at the Novo Nordisk Foundation Center for Biosustainability (DTU). Only time will tell what new, cool, and exciting discoveries will be made concerning this groundbreaking system! What else have you guys heard? Comment below!

Microbial Tape Recorders: A new Application to CRISPR

Research in the new gene-editing technology CRISPR has raised many red flags and ethical dilemmas as its full capabilities prove to be more than what was thought previously possible. It is used by bacteria to combat viral infections, but now scientists have repurposed it to keep records of a given bacteria’s environmental conditions, which could have significant applications to accurate chronicling of biological changes. Scientific American’s article, “Bacterial ‘Tape-Recorder’ Could Keep Tabs on Bodily Function” outlines how CRISPR “is a DNA sequence that makes and keeps a genetic record of viruses the bacterium encounters, commanding it to kill any that try to reinfect the bacterium or its descendants”. This natural function of bacteria, though, can be manipulated so that instead of exclusively accounting viral encounters, any environmental abnormality can be captured by CRISPR. More specifically, the bacterial mechanism would sense a special signal from a change in its surroundings and create trigger DNA, which, according to the U.S. National Library of Medicine, is a noticeable sequence of DNA from the invaders, which could be used to identify what exactly caused the change.

Applications of this technology today are far-reaching. This technology can be theoretically used to measure contaminants in fresh water or saltwater, or the nutrient levels in topsoil, but the predicted first application will be in monitoring bodily function in humans, and other animals. Digestion problems seem likely to be the first human system monitored with this new tool. Fructose Malabsorption is a digestive disorder which results in high levels of fructose sugar remaining in the digestive system. This disorder results from damaged intestines, normally from serious infection. Sugar levels in the digestive tract can now be monitored precisely by using this application of CRISPR in Escherichia coli cells (bacteria which are naturally found in the human digestive system). The record of sugar can identify specific problems diseased patients, after the E. coli cells are recovered from a patient’s feces, and cause them no harm in the process.

This tool is not without its drawbacks. It is reported that millions of modified bacteria need to be placed in a given system to have an accurate reading of environmental surroundings, and these bacteria have to be in the region of interest for at least six hours. The magnitude and duration of this prospective tool leave much to be desired as initial costs would be enormous, and other limitations, which can only be found through proper testing, remain unknown. In all, this advanced tool still seems applicable for now on only a small scale, but it is an example of CRISPR as a tool for good, and shows much hope for the future.

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Escherichia coli bacteria which can be modified with CRISPR to become a “tape-recorder” of the human digestive system

First step to recovery after uncontrollable wildfires: Microbes?

As we all know, wildfires all around the world, especially out west have been burning uncontrollably. They are continuing to get larger and more unpredictable. But these fires are not only affecting humans and animals, rather they have narrowed down to affecting the tiniest of forest organisms—including bacteria and fungi– and researchers are now finding that some of the microbes are “thriving”.

A study last week reported that “that populations of several bacterial and fungal species increased after severe wildfires in the boreal forests of the Northwest Territories and Alberta in Canada.” Studies like these and others such as the effect of smoke on the distribution of microbes, “give researchers a clearer picture of how wildfires change microbial communities”, and can possibly help them predict how ecosystems will recover after blazing flames. “Microbes help to maintain ecosystem health by decomposing organic matter and readying nutrients for plants to absorb”. For example, because certain fungi and bacteria have specific relationships with plants, it makes it possible to predict which nutrients will be available in an area.

Image result for wildfireIn order to test what they had predicted researchers collected samples from 62 sites about a year after 50 of them had been damaged by fire in 2014 in forests of two Canadian provinces. They found that certain bacteria in the Massilia and Arthrobacter genera were more present after than before the fires. This bacteria usually shows up in cucumber root and seed, and some researchers are predicting that there might be some growth of vegetation of that kind in the future when the forests begin to recover.

It is predicted that microbes “use fire to colonize new territory is by hitching a ride on small particles of ash or dust in plumes of smoke”. In a study published last November, Leda and her team conducted a study and found that “the microbes present in the smoke differed from those lingering in ambient air”. The microbes getting caught in the smoke she predicts can help plant growth in faraway regions.

There is a downside. It has been detected that some fungus, such as Phytophthora ramorum, cause sudden oak death. Another negative is the smoke that the firefighters, other ER personal, and people inhale after and during the fires could contain hazardous microbes. These can lead to lung problems and allergens.

Microbes are not often spoken about when wildfires sweep through, but they surprisingly have more impact than you may think. When entire ecosystems are reduced to ash, microbes determine the first step on the road to recovery.

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

Two Parent Burying Beetles in a Dead Rodent! Gross!

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

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

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

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

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

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

Message Intercepted – Commence attack on bacteria!

Tevenphage – Photo credit to Wikimedia Commons

While experimenting, a group of scientists noticed that a A virus, VP882, was able to intercept and read the chemical messages between the bacteria to determine when was the best time to strike. Cholera bacteria communicate through molecular signals, a phenomenon known as quorum sensing, to check their population number.  The signal in question is called DPO.  VP 882, a subcategory of bacteria’s natural predator, the bacteriophage, waits for the bacteria to multiply and is able to check for the DPO.  Once there is enough bacteria, in the experiment’s case they observed cholera, the virus multiples and consumes the bacteria like an all-you-can-eat buffet. The scientists tested this by introducing DPO to a mixture of the virus and bacteria not producing DPO and found that that the bacteria was in fact being killed.

The great part about VP 882 is it’s shared characteristic with a plasmid, a ring of DNA that floats around the cell. This makes it easier to possibly genetically engineer the virus so that it will consume other types of bacteria. This entails it can be genetically altered to defeat other harmful bacterial infections, such as salmonella.

Ti plasmid – Photo credit to Wikimedia Commons

Current phage therapy is flawed because phages can only target a single type of bacteria, but infections can contain several types of different bacteria.  Patients then need a “cocktail” with a variety of phages, which is a difficult due to the amount of needed testing in order to get approved for usage.  With the engineering capability of using a single type of bacteria killer and the ability to turn it to kill bacteria, phage therapy might be able to advance leaps and bounds.

As humans’ storage of effective antibiotics depletes, time is ticking to find new ways to fight bacterial infections.  Are bacteriophages and bacteria-killing viruses like VP 882, the answers?

The Effects of Non-Antibiotic Medication on Human Gut Flora

This article focuses on the effect of non-antibacterial drugs on human gut flora. The study published by the European Molecular Biology Laboratory (EMBL) in Germany tested nearly 1200 drugs, some 835 of which were designed to target human cells, to see if they had any effect on the human gut flora. The team discovered that 27% of these drugs had an effect on the gut flora.

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Example of Human Gut Flora

However, these effects are not necessarily bad. They suggest that some of these changes may be some of the positive side effects of these drugs. The researchers also found a connection between the bacteria not directly affected by the drugs and antibiotic-resistant bacteria.

What are the consequences of such a discovery?

Although the results of the study did not answer the question directly, there could be a link between non-antibacterial drugs and antibacterial resistance. The study’s coauthor, Kiran Patil, says that such effects “should be looked at very seriously”.

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Ultimately the study highlights the importance of considering the drugs put into the human body and what effect they may have – positive or negative – on the human microbiome. Personally, I think that people in this day and age overuse drugs, popping anti-inflammatories and headache pills like they are candy. This has only decreased our sensitivity to these drugs and caused a need for stronger and stronger drugs. We often don’t consider what these powerful drugs are doing to our delicate and complex microbiomes.

What do you think of the results of this study? Is it something to be worried about or just trumped up malarkey?

An Exception to Microbiome Functionality

A recent study was developed to understand how HIV corresponds to the microbial communities of the female sex organ. Dr. David Fredericks- a physician and college professor that teaches “Allergy and Infectious Disease” at University of Washington, led a study on the relationship between the diversity of bacteria in the vagina and how it may lead to HIV. The research population specifically focused in on sub-Saharan African women, who make up 56% of the continent’s infected population.

HIV-infected T cell

Scientists have come to discover that the greater the diversity of a microbiome, the more equipped that region of the body is for combating infections. Although- this concept is strictly relative to the mouth, intestines, and nasal passageway because a variety of bacteria inhabiting a vaginal microbiome can be very detrimental to a woman’s health. One of the leading risks from having a diverse vaginal microbiome community is the “human immunodeficiency virus”.  This virus can be transmitted through sexual contact, childbirth, nursing, or the usage of unsanitary needles. One’s immune system is weakened after contracting HIV because CD4 cells are damaged, which makes it harder for the body to fight off illness. Dr. Fredericks has revealed that the presence of a microbe called Parvimonas Type 1 is usually not a dangerous bacteria, yet the microbe is linked to the virus when there is a higher concentration of it in the vaginal microbiome.

Dr. Fredericks accomplished making this new find by using a strategy called the “dose-dependent effect” to measure the amount of “bugs” in a microbiome community in correlation to the risk of contracting HIV. In doing so, the scientists took cultures from 87 women who were infected with HIV and 262 cultures from women who tested negative for HIV to compare the bacterias found in both microbiomes. During the second half of the study, biologists used screening through a method called “PCR“and identified 20 types of bacteria that could potentially be linked to the virus. The bacterias involved in generating the virus in the female reproductive system were narrowed down to seven specific strains of rogue bacteria. Since the discovery, the biggest question revolving around HIV is determining how to permanently reduce the concentration of these illness-inducing bacterias.

What are Biofilms?

 

Biofilm being formed. (Pixnio)

Medicine has made great advancements in patient care and treatment over the last decade. However, everyday viruses and bacteria alike have become stronger and more resilient – even to the latest antibiotics. One such threat that has led to “…thousands of deaths…” in “…American Hospitals alone…” are biofilms. These bacterial cells “…gather [together] and develop structures that bond them in a gooey substance…” insulating them from the outside world. Biofilms ability to become impervious to antibiotics at a moment’s notice has led biologists to wonder both how they develop, and how to stop them.

To find out how and why these bacteria form biofilms, researchers at the Levchenko Lab, at Yale University, as well as from the University of California – San Diego, “…designed and built microfluidic devices and novel gels that housed uropathogenic E. coli cells, which are often the cause of urinary tract infections. These devices mimicked the environment inside human cells that host the invading bacteria during infections.” From this experiment, the scientist discovered that the bacteria would multiply until physical constraints inhibited them from further reproduction. At this point, the bacteria would become “stressed” and thus this “stress would induce the formation of a biofilm.

With the numerous mimicking devices that the researchers utilized in the experiment, they can now create many biofilms in predictable ways, and further analyze their behavior in similar environments. “This would allow for screening drugs that could potentially breach the protective layer of the biofilms and break it down.”  It is an amazing solution to a stubborn and persistent biological threat, that has already robbed enough, otherwise healthy, people of their lives.

It is imperative that we continue to make great strides in the advancement of medical technologies and treatments, as this will enable us to live healthier, more disease-free lives for the future to come. As viruses and bacteria get stronger, we need to make sure to keep up.

This Easy Method Will Make Sure You Never Get Strep Again

More than 3 million people a year get diagnosed with strep throat, however since it is a minor illness that is very easily treated, people do not see the issue with getting sick almost every year. Because bacteria reproduce in just a few days, many generations of bacteria go by very quickly; and every time they reproduce, they are also evolve.  Meaning, every time one takes antibiotics, the bacteria becomes more and more resistant to it, until we can’t kill them anymore with the same antibiotic.

For many humans around the world, the thought of not being able to fix a simple bacterial infection with an antibiotic is quite frightening; however recent discoveries about the human microbiome puts this fear away.

Bacteria at the microscopic level

There are many helpful bacteria that live in the throat and mouth. Most of these helpful bacteria are probiotics.  The probiotic that specifically attacks strep, is actually another strain of strep called Streptococcus salivarius K12. This probiotic produces two lantibiotics that attack Streptococcus pyogenes, the species that are responsible for the known strep throat.

From this knowledge, scientists did an experiment that gave one group a tablet that, when chewed, released billions of colonies of S. salivarius K12 and gave another group a tablet that did nothing. The group that received the probiotic, showed a 90% reduction in strep episodes than the group that received nothing. This information also helped decrease the time on antibiotics for strep by 30 times.

You can buy doses of S. salivarius K12 here if you are interested in not only staying away from strep throat, but also improving your overall oral microbiome.

If you are interested in reading more about not just the mouth and oral human microbiome, but the whole entire human microbiome; click here!

 

Genetic Engineering will Create Super Humans?!

“Synthetic microbiome? Genetic engineering allows different species of bacteria to communicate”

Before seeking to analyze how genetic engineering enables the alteration of the microbiome, it is essential to understand the nature of the microbiome. Humans’ microbiomes consist of “trillions of microorganisms (also called microbiota or microbes) of thousands of different species.” Initially, peoples’ microbiomes are solely determined by their DNA; however, as time goes on, a person’s microbiome can be shaped by other factors, including the environment in which they live, or their diet. The microbiome contains both helpful and deleterious microbes, but “In a healthy body, pathogenic and symbiotic microbiata coexist without problem.”

According to researchers from the Wyss Institute at Harvard University, Harvard Medical School (HMS), and Brigham and Women’s Hospital, it may now be possible to create a “synthetic microbiome.” The team did a study in which they utilized a particular type of quorum sensing known as acyl-homoserine lactone sensing. Quorum sensing allows bacteria to regulate the expression of genes and to detect the size of bacterial colonies, through signal molecules. First, the team inserted “two new genetic circuits into different colonies of a strain of E. coli bacteria.” One of the circuits acted as a “signaler” and the other acted as a “responder.”

File:E. coli Bacteria (16578744517).jpg Picture of E. Coli bacteria

In short, the team inserted a single copy of luxl, a gene activated by the molecule anhydrotetracycline (ATC), into the signaling circuit. The signaling molecule formed by this gene then binded to the receptor circuit, which activated another gene, known as cro. The cro gene creates Cro proteins, and these proteins triggered a “memory element” within the responder circuit, in which two more genes, LacZ and another cro, were produced. If the signaling molecule is received (which it was), the presence of LacZ causes the bacterium to turn blue. Most importantly, the additional cro gene essentially keeps the “memory element” on, so this cycle continues.

To make sure that this system works in living organisms, the researchers tested it in mice. Signs of signal transmission in the mouse’s gut between the signaler S. Typhimurium bacteria and E. coli responder bacteria were detected. In other words, the engineered circuits allowed the bacteria to communicate with one another.

While these findings are extremely exciting, scientists have yet to discover whether or not other genetically engineered species of bacteria will also be able to facilitate communication between molecules. A Founding Core Faculty member of the Wyss Institute said that “[They] aim to create a synthetic microbiome with completely or mostly engineered bacteria species in our gut, each of which has a specialized function.” If this is achieved, we will move one step closer to becoming super humans!

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60 Million Year Old Farmers

Microbial ecologist Cameron Currie of the University of Wisconsin-Madison has made an intriguing discovery about the lives of some South American leaf-cutter ants. He found that long before humans cultivated fruits and vegetables for food ancient leaf cutter ants where cultivating fungus. The ants farm the fungus as a food source, but there are pathogenic bacteria that can kill the fungus. To thwart these malicious bacteria, the ants have formed a symbiotic relationship with a different bacteria known as actinobacteria. These actinobacteria fight off the pathogenic bacteria and protect the fungus.

File:Leafcutter ant.jpg

Leaf Cutter Ant

But how could we possibly know if fungal-farming ants existed millions of years ago?

File:Baltic amber inclusions - Ant (Hymenoptera, Formicidae)10.JPG

Ant Trapped In Amber

Well, I am glad you asked. Curries research focused on a 20-million-year-old sample of amber that had a few of these green-thumbed ants trapped inside. The ants had specialized pockets in their heads called crypts where the ants store these actinobacteria. These leaf cutter ants are walking pharmaceutical factories.

It is intriguing that some of the smallest insects on the planet where farming and cultivating food millions of years before we even thought of it. Not only that, but they have been using anti-biotics for millions of years whereas humans have only started using them 60 or 70 years ago.

What lessons do you think humans today can take away from these ants? Could they be the key to our anti-biotic overuse crisis?

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!

CRISPR Defends Bacteria, and Helps Scientists Discover New Bacterial Defenses

Although CRISPR is known for being a gene-editing tool, it can be used in other areas, such as a defense mechanisms in bacteria. This discovery “Probably doubles the number of immune systems known in bacteria,” according to a microbiologist at the University of California. Bacteria have to defend themselves against Phages, which take control over bacteria’s genetic machinery and force them to produce viral DNA. Bacteria use CRISPR to defend themselves against Phages because it stores a piece of past invaders DNA so bacteria can recognize and fight of those future viruses.

 

Photo By J LEVIN W (Own work) [CC BY-SA 4.0 (https://creativecommons.org/licenses/by-sa/4.0)], via Wikimedia Commons

the researchers found that nine groups of bacterial genes were defense systems, and one system protected against plasmids. The data revealed a possible shared origin between bacterial defense systems and defense systems in more complex organisms. Some of the genes contained DNA fragments that are also  important parts of the immune system in plants, mammals, and invertebrates. The discovery of more bacterial defense systems poses the question of wether they will also be useful biotechnology tools like CRISPR is.Only 40% of bacteria have CRISPR, so scientists searched for other bacterial defense mechanisms. To do this, they looked at genetic information from 45,000 microbes, flagging genes with unknown functions located near defense genes, because defense-related genes cluster together in the genome. The researchers then used genomic data to synthesize the DNA and  inserted them into Escherichia coli and Bacillus subtilis, which can both be grown and studied in the lab. They then studied how well bacteria defended themselves during phage attacks with various genes detected. If eliminating certain genes deterred the bacteria’s defense, that determined that those specific genes were a defense system.

 

For more information, click here. For more information on CRISPR’s role in bacteria, click here.

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