BioQuakes

AP Biology class blog for discussing current research in Biology

Tag: bacteria (Page 1 of 3)

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.

This Parasite Can Change Agriculture for the Better

When parasites take control of a host, it may seem like all is lost for the unfortunate animal. However, a newly discovered parasite uses a mechanism that actually slows down plant aging, and may offer new ways to protect crops that were once threatened by diseases. 

Prior to this discovery, very little was known on how this parasite functioned on both a molecular and mechanistic basis. The Hogenhout group at the John Innes Centre and collaborators published in Cell have identified a manipulation molecule produced by Phytoplasma bacteria, which hijacks the development of plants. This protein breaks down key growth regulators, which as a result causes abnormal growth.

According to an article published by FronteirsIn, phytoplasmas and their associated diseases cause severe yield loss globally. For example, Aster Yellows cause major yield losses in crops such as lettuce, carrots, and cereals. As stated in the article, “Phytoplasma diseases of vegetable crops are characterized by symptoms such as little leaves, phydolly, flower virescence, big buds, and witches’ brooms.” These effects ultimately cause the host plants to die over time. 

Phytoplasma Growing on a Plant

Professor Saskia Hogenhuot said that “Our findings cast new light on a molecular mechanism behind this extended phenotype in a way that could help solve a major problem for food production.” One of these findings includes the bacteria protein entitled SAP05, which manipulates the plant’s molecular structure. This manipulation targets the process of the proteasome, which breaks down obsolete proteins inside plant cells. SAP05 causes the plant proteins that are used for regulating growth and development to be thrown out. With the absence of the proteins, the plant’s development favors the bacteria, which in turn triggers vegetative growth and pauses the plant’s aging process.

Specifically, SAP05 directly binds to the plant developmental proteins and the proteasome. Proteasomes hold a very important role in the cell regarding the degradation of proteins, with Professor Gonzalez writing, “proteasomes perform crucial roles in many cellular pathways by degrading proteins to enforce quality control and regulate many cellular processes such as cell cycle progression, signal transduction, cell death, immune responses, metabolism, protein-quality control, and development.” Conversely, SAP05’s direct binding is a newly discovered method of degrading proteins, unlike the usual fashion of proteins degraded by proteasomes that are tagged with ubiquitin beforehand. 

To further study SAP05, the research team wanted to see if SAP05 affects the insects that carry the bacteria plant to plant. Turns out, SAP05 does not affect the insects due to the structure of the host proteins in animals differing enough from plants. This research also enabled the team to identify the two amino acids in the proteasome that interact with SAP05. If these two amino acids in the plant proteins were switched to the amino acids found in the insect protein, they would prevent abnormal growth. 

In a polypeptide chain, every amino acid is important to how the chain functions. Specifically, an amino acid’s unique side-chain gives it different characteristics, which plays a role in how the protein is structured and its function in the cell. In this case, these two amino acids from plant to insect proteins ultimately change the way SAP05 interacts with the polypeptide chain, which as a result changes the effect. 

Personally, I feel that this discovery is groundbreaking since it enables countless possibilities regarding the prevention of mass yield loss. How do you think this research will be utilized in the future? Let me know in the comments!

A Sweet Post About Sourdough!

When Covid-19 hit the US, some of the biggest quarantine coping mechanisms all revolved around a fan favorite carbohydrate: bread. With the copious amount of time on people’s hands, baking sourdough bread was the perfect activity.

Unlike any other bread, it’s hard to get the perfect tasting sourdough. Research has found that there are biological reasons behind sourdough bread and its taste, but before doing so, it’s important to learn what sourdough bread is made up of, and how it’s made. To help learn more about the process of making sourdough bread from scratch, I got a mini crash course from Little Spoon Farm. The starter (initial mixture) contains flour and water and sometimes salt, which will eventually grow into a diverse selection of microbes (these are tiny living organisms, which in this case are bacteria). The starter has to sit for 7-14 days, and within that time, the starter grows through the flour by eating the sugars within itself. With that growth comes bacteria/microbes and lactic acid, which eventually will allow the bread to be able to leaven in the oven.

Recent studies have shown that each starter is made up of different microbes. One study had 18 professional bakers from all around the globe make their sourdough, and send it to a lab in Belgium, where DNA sequencing was used to identify the microbes in the different starters. Although there were common yeasts and acids found like Saccharomyces cerevisiae and Lactobacillus, the strands and amount of each differed according to the starter. Another study done by Elizabeth Landis, at Tufts University, looked at 560 different starters submitted from all around the world. Through doing so, she found recurring microbe groups within these different sequences. There is still no definitive reason behind the microbe groupings, and why exactly they differ for each starter, but Landis mentioned that certain yeasts “specialize in feeding on distinct sugars,” due to the fact that they are made of different sugar mixtures. Some yeast also lack certain enzymes, which as we learned in class, help break down molecules. In this specific situation, the enzymes within different yeasts feed on and break down sugars. Differing yeasts could also be a reason why sourdough bread has different flavors. (Keep in mind that Landis’ findings are still under review, so there are still limited details on this experiment and not definitive reasoning).

Microbial ecologist, Erin McKenny, further elaborates on how “each microbial community can produce its own unique flavor profile.” For example, when more acetic acid is present in the starter, the bread will have a more sharp and vinegary taste. When the starter produces more lactic acid, it has a more sour and yogurt like taste. Metabolic byproducts within the starter could also potentially add to the complexity of the sourdoughs’ taste. In addition to each microbial community, scientists have identified other features that influence the taste of the bread like temperature. When lactic acid ferments in a warmer area, the bread has a more sour taste, and when it ferments in a colder area, the bread has a more fruity taste.

After looking at multiple articles showing how bakers get their sourdough to have a certain taste, I have learned how important the specifics are when it comes down to making sourdough. One article that gave tips on how to manipulate the taste of sourdough reinforces everything that the main article helped explain, and talks about the importance of keeping a warmer, dry climate to ensure that the bread tastes sour. It turns out that a quarantine treat may be a bit more complex than it appears. It’s interesting to see how biology plays a key role in one of the most prominent foods, and next time you consider making sourdough or get a bread basket from the Cheesecake Factory, you’ll now know the biology behind it.

Did ants originate from zombies? This fungus will give you the answers.

There is a certain fungus that turns ants into zombies, but afterward, they explode. When ants are just walking by minding their own business they step on fungal spores. It attaches to the ant’s body and the fungal cell goes inside of the ant. The fungus feeds from within and increasingly multiples cells and it is called, Ophiocordyceps,   mainly living in the tropics. The danger about this fungus is that the ant is unaware of this whole process, it goes about its daily life, searching for food and bringing back to its nest. However, the fungus takes up half of an ant’s body mass. It undergoes a parasitic relationship where the fungus benefits, while the ant is harmed.

Once the fungus is done feeding, the ant will feel a needle-like sensation. What is happening here is that the fungus is pushing on the ant’s muscle cells. And the cell signals also get sent to the ant’s brain, then the ant will climb upwards above its nest. Ophiocordyceps does something very weird where it allows the ants to move upwards to a leaf above ground and then the ant bites down, where it locks its jaw. Then it sends out “sticky threads that glue the corpse to the leaf.” The ant’s head then bursts open, called a “fruiting body”, where it looks like horns projecting from the ant’s heads and the horns disperse more of these fungal spores onto its nest below it leaving behind a trail of spores. 

Hornlike antlers that come out of the ant’s head

There is still so much that is unknown about Ophiocordyceps because scientists don’t even know what kind of chemical gets into the ant’s brain causing it to climb. There are ants that age back to 48 million years old gripped onto leaves.  Scientists thought there was one species that zombified ants but it turns out there are at least 28 different fungal species that attack other insects as well. Dr. Araújo drew out a family tree to see what was infected by Ophiocordyceps. It became known that all Ophiocordyceps species come from a common ancestor, first infecting beetles larvae, not hemipteran.

The beetles that are affected by the larvae live in eroding logs.

“They’re mostly solitary creatures, with a very different life history,” compared to ants, she said.

It can now be inferred that possibly millions of years ago when this was happening to beetles, ants picked up the fungus if they were living in the same logs. Thus a constant cycle and more spreading of fungal spores. Even though natural selection favored keeping the ant’s host healthy and away from parasites, Ophiocordyceps had to find a way to make the ant leave the nest, not far enough from its environment, but just in the right place to send out the spore to infect whatever other ants were living around it. 

Because this behavior is so unordinary it is not possible that only one gene is responsible for all of this. They keep finding new species. Dr. Hughes and Dr. Araújo are still researching to find that there are hundreds of other species of Ophiocordyceps that are yet to be discovered.

Exposure to Certain Bacteria Can Lead to the Development of Celiac Disease

In a study published by the Nature Structural and Molecular Biology, researchers have found that bacterial exposure is a potential environmental risk factor, leading to the development of Celiac Disease. Scientists believe that this discovery can lead to diagnostic or therapeutic approaches to the illness.  

Celiac Disease affects about one in 40 Australians and about half are born with about one of two genes that cause the disease. People suffering from Celiac Disease must follow a strict non-gluten diet, as any amount of gluten can trigger health problems. Scientists have known for a while that environmental factors trigger Celiac Disease, alongside the genetic predispositions, but were unaware of exactly what the environmental causes was.

To conduct the study, researchers showed how, at a molecular level, receptors that were isolated from immune T from Celiac Disease recognized pieces of protein from certain bacteria that mimic gluten. The results showed that exposure to such bacteria may play a role in the recognition of gluten by the same T cells when individuals with a predisposition eat any amount of gluten. Thus, the individual’s immune system reacts to the bacteria molecules and, in doing so, develops a reaction to gluten molecules because to the immune system the molecules are identical. 

With these results researchers have now linked microbial exposure as a possible environmental risk factor for Celiac Disease through a molecular foundation. 

The results of this study is extremely important as it can lead to new search in Celiac Disease and possibly new methods of prevention!

Human Microbiome and Age: A Complex Balancing Act

 

Dozens of studies in the past few years have been dedicated into research on the bacterial microbiome that lives inside of every human being. The cultivation of the microorganisms that live symbiotically inside of us begins as soon as a baby comes out of the womb and is exposed to the world outside of its mother’s uterus. These bacteria are imperative to many, many bodily functions throughout our lives. The link between us and our microbiome is so crucial that a faulty microbiome can easily cause death. An example of how these bacteria are so important is the fact that many molecules we use daily are mainly created by symbiotic bacteria such as Vitamin B and Vitamin K, 75% of which is supplied symbiotically.

 

The Link Between our Gut and Age

There is a lot of research left for scientists to discover the effects of our microbiomes but one of the most hotly studied aspects of the bacteria that inhabit our gut is their relationship to our age. There is much research showing how our specific colony of bacteria changes over time. One study by Alex Zhavoronkov shows that the specific type of bacteria present at various stages of development stays consist across different people. So consistent in fact that he was able to have a computer teach itself how to predict the age of a subject within 4 years of accuracy based on their microbiome. He noted that of the 95 bacteria he studied, 39 were crucial in determining the age of a subject. This research seems to suggest that the bacteria in our stomach could serve as an accurate biological clock which could be used to analyze the effects of various things such as alcohol consumption, diet and disease have on a persons longevity. The main issue with his study though is that his subjects all represent a sliver of the human population and due to bacteria’s great biodiversity, predicting ages across the globe could be impossible. Yet in any case, the link between our microbiome and our age is certainly a huge possibility.

Can Bacteria Reverse Aging?

No. Bacteria cannot reverse the aging process unfortunately. We simply do not have   enough research and understanding of the link between age and the microbiome inside the human body enough to make such a grand statement. However, one study seems to suggest a chance in this strange idea. In this unorthodox study, the microbiome of young Turquoise Kill Fish was added to the microbiomes of older fish of the same species. The results are surprising. The older fish ended up living lives 37% longer than their unaffected counterparts. The reasons are unclear yet the evidence is stark. Could this mean we could put young bacteria into humans and continue to stretch our lifespans to be longer than 100 years? Again, we do not know but only the future will tell what will happen.

Are Antibiotics Truly Good?

Antibiotics are also known as antibacterials. They can destroy or slow down the growth of bacteria in the body. They’re used to fight against certain infections that attack the immune system. Although the use of antibiotics can save a person’s life, the use of them can have repercussions. Most gut bacteria can recover quickly from the use of antibiotics, however there can be long-lasting effects. The changes it makes isn’t necessarily harmful, but that isn’t always the case. 

 

The gut microbiome, has roughly 10 trillion to 100 trillion bacteria and other microorganisms that live in the digestive tract, contributes to health by synthesizing vitamins, metabolizing drugs and fighting pathogens. Anything that disrupts the balance of microorganisms, such as antibiotics, which can kill both “good” and “bad” bacteria, has the potential to cause disease.” 

Research done in a 2016 study shows that being exposed to antibiotics as an infant can alter the gut microbiome in a baby and “weaken the immune response for years to come.” The duration of breastfeeding reduces the frequency of infections, and the risk of being overweight. Conclusions of the study conveyed antibiotic use in a child during the breastfeeding period could weaken the beneficial effects of long term breastfeeding. In addition, the results suggest that intestinal microbiota is affected by the long term metabolic benefits breastfeeding has. 

Antibiotics are the most common type of medicine prescribed to young children in the Western world. As mentioned previously, antibiotics can dramatically alter the gut microbial composition. Research shows, “…the gut microbiota plays crucial roles in immunity, metabolism and endocrinology, the effects of antibiotics on the microbiota may lead to further health complications.” Exposure to environmental microorganisms and parasites is important for healthy development and maintenance of the immune system. In Western countries contact with microorganisms has significantly decreased over the recent decades. “ As antibiotics are a factor that reduces exposure to microorganisms and disrupts the body’s natural microbiota, this… may help explain the observed effects of antibiotics on the immune system.”

“Since infancy is a crucial time for microbial establishment, it is necessary to evaluate the influence of antibiotics given quite liberally during this period. Antibiotic treatment given to both infants and toddlers has already been shown to strongly affect microbiome composition. In an attempt to understand the effects of antibiotics on the microbiome, both human reports and experiments in animal models have been employed”.

Although, antibiotics are a powerful source of medication that can fight off infections and save lives when used properly, it is essential to not overuse or become too reliant on them. Overuse contributes to the resistance to fighting bacterial infections, and hurts the body’s natural microbiota.

 

CAP v.s. HAP: Pneumonia in the Microbiome

While many may not know this, there are various types of pneumonia.  The most common variant, CAP (community-acquired pneumonia), is the most prevalent strain of the infectious disease.  As the name may suggest, CAP is acquired through daily interactions (whether that may be contact or inhalation of pathogens which could later travel to the lungs) with any surface that has bacteria such as Streptococcus pneumoniae and Haemophilus influenzae.

While pneumonia is a well-known infectious disease among the population in 2019 due to the plethora of literature and research done on it, most people do not know that other variants of pneumonia are contracted in different ways, through different strands of bacteria.  HAP (hospital-acquired pneumonia or healthcare-associated pneumonia) can be contracted from extended periods of time in a hospital, nursing home, or rehabilitation center.  This pneumonia variant is a result of the P. aeruginosa and Staphylococcus aureus bacteria, which are completely different from the bacteria that cause CAP.

The demographics of people who suffer from each of these variants appear to be mostly similar with the only difference being that CAP has a stronger association with COPD whereas HAP still has an association with COPD, but in a smaller portion of the demographic.  Similarities between the two are the increased risk if one uses tobacco products or suffers from COPD, however, aside from these shared risk factors, the two variants are different in treatment methods (effectiveness of certain antibiotics) and contraction.

Relative to the microbiome, the major differences in the diseases can be found when testing biomarkers.  According to Ann Transl and Thomas Tschernig of the “Annals of Translational Medicine”, “lower levels in HAP as compared to CAP were found for MMP-8 and soluble E-selection, higher levels in HAP as compared to CAP were found for protein C”.

The significance of this discovery lies in the fact that the different variants of pneumonia could not be prevented, diagnosed, or treated in the same ways, thus exemplifying the dangers that would arise if the different variants were not classified and identified.

Additional resources.

 

 

Discovering and Using Your Personal, Biological, Tiny Army

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

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

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

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

File:Immune Response to Exotoxins.png

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.

https://commons.wikimedia.org/wiki/File:E._coli_Bacteria_(16578744517).jpg

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?

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