BioQuakes

AP Biology class blog for discussing current research in Biology

Tag: human gut microbiome

Could A Computer Detect Your Sick Gut?

Photo by Nicola Fawcett (photo source)

 

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

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

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

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

 

Parents Take Warning: Antibiotics Can Be Harmful to Infants

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

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

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

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

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

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

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

How does this research change your perception of antibiotics?

 

No More Lactase Pills?!

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

Bifidobacteria in human gut microbiome

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

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

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

 

More Bacteria than Human?

The well being of humans is best when we are cooperating with others whether that be other humans or bacteria inside of us. According to Matthew Bull “the human gut microbiome and its role in both health and disease has been the subject of extensive research, establishing its involvement in human metabolism, nutrition, physiology, and immune function.” An imbalance in our microbiome will often result in some type of sickness so it is very important to keep our guts healthy. It is likely that there are more bacteria cells in our gut than there are our own cells. So in this image right here  there would be more bacteria cells than human cells. Some people even consider the microbiome a bacteria ecosystem that just happens to be in our gut. While this may sound bad, these bacteria often break down food for us and supply us with energy needed to do daily activities. It is truly fascinating to think that we have many living things inside of us that may even outnumber what is actually considered “us”. But is it possible for these bacteria to take over our bodies? The answer is probably no…we hope, but if we continue to eat well and stay healthy these bacteria should continue to help us. However, if we eat poorly and don’t stay healthy these bacteria can end up being a problem for use. So at the end of the day eating health helps the relationship between us and the bacteria inside of us stay healthy and lets us stay healthy.

The diet that we should have to keep a healthy relationship with these bacteria involve eating less sugar and fat and eating more fiber. A diet with a lot of fat and sugar but little fiber can lead to illness. It is also best to stay away from eating a lot of iron. There are some things that help our microbiomes such as milk, milk has proteins in it that help keep our microbiomes health. So eat less sugar, bad fats, and iron and eat more fiber and drink more milk.

 

New Discoveries Link Stomach Bacteria with Autism

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

Mycobacterium tuberculosis Bacteria, the Cause of TB

Image Source

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

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

Original Article

Further Reading:

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

 

It’s Time to Re-program the Human Gut

(Photo of the human gut (licensing information here)

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

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

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

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

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

Source: Biology News

Bringing the Human Gut Microbiome into the Light

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

 Escherichia coli

E. Coli 10000x magnified

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

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

 

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

 

Main Article:

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

 

Other Articles:

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

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

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

Sewage Does More than Just Gross You Out… It Carries a Signal For the Microbiomes of Humans

Who knew that sewage would ever be useful. Well, it is a successful way to collect fecal bacteria from people. It can monitor, through gut microbes, the public health of a population without invading people’s privacy. The human gut microbiome consists of huge amounts of bacteria in the gastrointestinal tract. This gut bacteria has important functions in a healthy human. Recently, there has been much attention to the human microbiome, and more specifically, finding a “healthy microbiome” by identifying which bacterial communities are associated with healthy individuals. What has been hindering this experiment are financial concerns but also privacy concerns in terms of the individuals that can be screened.

Researchers from MBL (Marine Biological Laboratory) and the UWM (University of Wisconsin-Milwaukee) School of Freshwater Sciences proposed the idea of using sewage as a population that consists of a signal for human microbiomes. The scientists used oligotyping to compare 137 healthy people’s gut bacteria (provided by the Human Microbiome Project) to the bacterial communities of more than 200 sewage samples from 71 different U.S. cities. Researchers realized that geographically distributed populations consists of a similar core set of bacteria and its members symbolize many different communities within U.S. adults. The percent of obese people in a city is used by the study as a measure of a lifestyle difference which indicates that this bacteria community structure is accurate in detecting obesity in a city. Lifestyle differences are important because they can change the human gut microbiome and an indicator of obesity is the microbial community composition. This process of working with microbiomes of individuals is similar to drawing a map of a specific geographical area and fishing out new understandings and patterns. If it weren’t for the sewage, the scientists wouldn’t have been able to differentiate the cities based on their level of obesity. This type of approach can be effective when it comes to answering concerns about public health, without undermining the privacy of individuals.

I found it interesting how this profound yet relatively small experiment is even part of a bigger plan to create better water pollution and public health assessments. Do you think it can lead a better water pollution and efficient public health assessments? Overall, it’s amazing how new technologies can aid in decrypting information from complicated environments. I’m excited to see where this experiment takes us as it leads researchers and scientists in a more knowledgeable outlook on our environment and in public health.

The original article can be found here.

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