Blog 15 - Antibiotic Resistant Germs

     I have been really interested in the Lechuguilla Cave lately, because it is very complex and contains a lot of mysteries. It stretches for nearly 1,600 feet! "The bacteria that grow on the walls of its most remote recesses have been living in complete isolation for more than four million years." 

   Gerry Wright, a microbiologist at McMaster University, came to New Mexico all the way from Ontario to preform experiments on the bacteria in the Lechuguilla cave. After culturing the walls and collecting the various bacteria in the cave, he doused them with different drugs that doctors have used for 70 years that can kill bacterial infections. But they bacteria from the cave wouldn't die. They were resistant to 14 antibiotics. 


"Antibiotics were introduced in the mid-1900s. Each time a new drug was introduced, it would take years before bacteria that could resist it became common." 

    This is very strange because usually a microbe has to be exposed to the antibiotic to become resistant. But they bacteria in the cave have been "cut off from the world" for centuries; never exposed to antibiotics. Scientists believe that antibiotic-resistance genes are an ancient part of nature.

    A new study from Dr. Nesme shows that these antibiotic resistant genes can be found in all environments around the world; from Antarctica to the bottom of the ocean. The question then arose, "If these genes are everywhere, what are they doing in bacteria?" Bacteria actually make their own antibiotics to fend off competitors, and can fend off their own poison.  Bacteria use these resistant genes that have nothing to do with antibiotics. What these bacteria use these genes for is unknown. 

This article was really cool to me. Writing these blogs help me learn something new about microbes every time. I wonder if scientists will ever find out what else bacteria is using the resistance genes for. The article was very well written and provided a ton of information, including two different studies from two different scientists. Way cool.

http://www.nytimes.com/2014/05/08/science/antibiotic-resistant-germs-lying-in-wait.html?action=click&module=Search&region=searchResults&mabReward=relbias%3Ar&url=http%3A%2F%2Fquery.nytimes.com%2Fsearch%2Fsitesearch%2F%23%2Fcave%2Bmicrobes%2F

Blog 14 - "Wild Yeast" Beers

     Since we are heading to the Brewery tomorrow, I decided to check around NY times for an article about beer making. I came across something really odd about the yeasts used by beer/wine maker, Chad Yakobson. It is called Brettanomyces. It is a ‘cousin’ of the domesticated, typical yeasts that are normally brewed with. Brettanomyces is known as “wild yeast” – “a reference to its natural habitat (fruit skins) and to its volatile temperament — “Brett,” as it is widely known, can lead to unpredictable fermentations and gushing beer bottles, aromas politely described as funky, and fear.” Usually brewers don’t want this type of yeast in their beer, and try there hardest to sterilize all the equipment; But not Yakobson. He says that this brings beer back to its roots, before there was sanitization. Brettanomyces creates a whole new category of beers – “Brett Beers.”

    Brewers who use this type of beer making shoot for something along the lines of a pre – WWII Belgian Brewery type beer. Instead of having a typical tasting beer, such as Budweiser, Brett beer’s flavor can vary greatly. The flavors intensify in the bottle, “as the yeast slowly metabolizes complex sugars.” Because the Brett beers are so unique and ‘funky’ brewers think they will never become a mainstream beer. It is also more expensive to brew Brett beer, and there is always a risk that the wild yeasts will contaminate other ‘non-wild’ beers.

    I enjoyed reading this article. It was amazing to see that using ‘wild yeast’ can change the flavor of the beer so drastically. There was really no argument in this article, but it did have a lot of really cool information. The quotes from actual Brett beer brewers helped inform the reader about what the beer is. Pretty cool stuff.

Blog 13 - Mapping the Great Indoors

   Not really knowing what to blog this week, I did a search on the good ole New York Times website; “Cave Microbes.” I was expecting, well, something about microorganisms in caves. But the key words pulled up an article related to microbes indoors. Weird, right?

   The article I found was actually pretty cool. It is about the microbiologist, Dr. Fierer, of Boulder, Colorado, and his studies of all the organisms that live in our homes. Fierer studies microbes in homes to, hopefully, come up with strategies to manage homes, and eliminate all the harmful species, and keeping all the beneficial ones. But first, they need to know what’s inside.

   “Here’s an undeniable fact: We are an indoor species. We spend close to 90 percent of our lives in dry walled caves.” In a typical home, you’ll find humans, dogs, cats, maybe fish, ants, bugs… and billions of microbes. Fierer swabbed 82 surfaces in 4 Boulder homes, and the all the results were similar; bacteria, staphylococcaceae, corynebacteriaceae, molds, species associated with raw produce, etc... I found this part a little crazy: “The microbes living on your pillowcase are not all that different from those living on your toilet seat.”

Fierer came to the conclusion that humans rapidly “infect” the places in which they live. We come in contact with 37 million bacteria per minute, just on our exposed skin.  Dr. Fierer teamed up with Rob Dunn from North Carolina State University, and sampled 1,400+ homes, and the results are still being analyzed.

  I liked this article, it was very well written, and had a lot of information. The intro to the article was cool because it sounded like a story. I had a few questions, like what corynebacteriaceae is, but that was it. This article’s audience was definitely for someone who knows about microbes because it had some terms that I would not have known without this class. Towards the end of the article there were questions that some people had, such as “If you live in a forest, do you have different microbes than if you live in a desert?” in which he replied with “These are questions we don’t have the answer to yet.” Overall good article, but rises a ton of questions.

http://www.nytimes.com/2013/05/28/science/getting-to-know-our-microbial-roommates.html?pagewanted=2

Blog 12 - Demodex Mites

   I was scrolling around the web looking for blog ideas when I came across something known as the Demodex Mite. These things are extremely weird, and a lot of people don’t know anything about them.

“They crawl around your face at night, feeding off your oil and skin cells. They have no anus, so eventually explode inside your hair follicles.”

Yeah, you read that right. And everybody has them. They are completely normal. Even though what they do is very odd. During the day they grow in size feeding off of skin cells and facial oil, then at night the female lay eggs inside hair follicles. When they end up dying, it causes skin inflammation and irritation. What else is gross is that they can be transferred just by touch.

“An overgrowth of the mites has been linked to conditions such as rosacea, where people over the age of 30 develop sensitive red lumps and bumps over their nose or the middle of the face.”

Because they are normal, you cannot just scrub your face because excessive cleaning can lead to other bacteria entering the skin. Just normal washing of the skin can help prevent these nasty things.

This article wasn't the best one I have read this year. It was the only article I could find other than sites like Wikipedia. It did provide a lot of general information, and it was not hard to understand. Anyone could read it for general knowledge about these mites. It had a few doctors talk about the mites to back up the information. But overall, a nice, general article.

http://www.smh.com.au/national/health/it-eats-your-skin-then-explodes-inside-meet-the-demodex-mite-20140414-36mfj.html

Blog 11 - Drug Resistant Bacteria Found in New Mexico Cave

Deep in the Lechuguilla Cave in New Mexico, microbiologists have discovered close to 100 types of bacteria that can fight off antibiotic drugs we use today.  The bacteria in the cave coat the walls, all the way down to 1,600 feet below the surface. Because it is so deep, any water that trickles through the surface takes roughly 10 thousand years to reach the caves depths!

    Even though the cave is covered with bacteria, most of it is harmless to humans.  They are completely resistant to antibiotics, including newer synthetic drugs. These microbes will help scientists understand how drug resistant diseases emerge.

    Lechiguilla is the deepest and largest cave system in Carlsbad. It is the seventh known longest cave (130 miles). Until 1986, it was untouched by human activity. Hazel Barton, a scientist from Northern Kentucky University, went in the cave and sampled biofilms. When tested with antibiotics, these strains (known as superbugs) “can immobilize, chew up, or block natural and synthetic antibiotic compounds.

   One of the biggest questions is which came first; Resistance or antibiotics? Were there originally natural antibiotics deep underneath the earth and bacteria grew resistant to it, or the other way around?

More research can help save time, and money; especially for pharmaceutical companies. If a company wants to invest a billion dollars in researching a single antibiotic, scientists should study and know if pathogens can build a resistance to it.

  This article was really cool, especially because it was from a cave here in New Mexico.  It was really well written, and had input from several scientists. I didn’t have any questions after reading it, but the audience is definitely for someone who knows general information about microbes and bacteria. 

http://news.nationalgeographic.com/news/2012/04/120411-drug-resistance-bacteria-caves-diseases-human-health-science/

Blog 10 - Algal Bloom Leads to Manatee Deaths

     Since I have focused most of my research on the Red Tide algae blooms this semester, this was an article I came across. For those of you who don’t know, The Red Tide Algae is a toxic bloom that occurs mainly in the Gulf of Mexico, it is pretty harmless to humans, but it is known for killing massive amounts of sea life. What I didn’t know, is that manatees are suffering greatly from it.

     Manatees are already an endangered species. There are only 5,000 manatees in the Floridian waters and 241 manatees have been killed because of these algae. Experts say the numbers are surely to rise. The dino flagellate microbes that make up the red tide live in warm waters, as do manatees, and the water in Florida is the place for that. Even though the numbers of red algae has dissipated, the toxins from it still live on the grasses and seaweed in the water, and manatees can eat 100 pounds of grass daily.

    Scientists are still puzzled to see why the toxin levels are so high. The brevetoxins can kill mammals, birds, aquatic life, and there have even been cases of respiratory problems in humans. Some think that the mild winters helped the algae live longer. “So far this year, at least 463 manatees have died from a range of causes, more deaths than had been recorded previously” (April 6, 2013). Most deaths tied to poison.

   

     This article was shocking. I couldn’t believe how many manatees have died from the brevetoxins, and scientists still don’t know what to about it. It contained a bunch of information about the problem, and was very well written. I didn’t find any information on this year’s death rates, but hopefully it has gone down, and scientists are coming up with ideas to help stop this problem.

http://www.nytimes.com/2013/04/07/science/earth/algae-bloom-in-florida-kills-record-number-of-manatees.html?action=click&module=Search&region=searchResults%230&version=&url=http%3A%2F%2Fquery.nytimes.com%2Fsearch%2Fsitesearch%2F%3Faction%3Dclick%26region%3DMasthead%26pgtype%3DHomepage%26module%3DSearchSubmit%26contentCollection%3DHomepage%26t%3Dqry953%23%2Fred+tide+algae&_r=0

Blog 9 - Interview with Michael Pollan

     Microbes are used a ton in making various foods and drinks; as you know, cheese and beer are the most popular. Brewers and cheesemakers are known as “fermentos”. These are the kind of people who have a very “relaxed attitude” towards bacteria; unlike most people.

     In this article the author, Rachel Nolan, interviews Michael Pollan, a food author. She asked him, “What surprised you most about the microbiome’s possible effects on humans?” Pollan replied with something I have never heard before. What surprised him (and me) most was that our gut microbes can actually obtain genes from our food, thus changing their genetic make-up. For example, people in American have different microbes than people in Japan, because they have a gene that lets them metabolize seaweed. This gene came from a microbe living on the seaweed.

    Rachel then asked Nollan how we can improve our micro biome, in which he responded with that humans should garden. Exposing one’s body to soil can increase “microbial pressure”. He also says that having a dog is good too.

    She continues asking Pollan various questions about micro biomes, but these are the most interesting. This article was very cool because instead of reading a normal article, it was actually an interview with an author of the book “Cooked”. Pollan did a ton of research on microbes, and the article provided a lot of information I didn’t know. The only question I had was what “microbial pressure” was. Overall, it was a cool read

http://6thfloor.blogs.nytimes.com/2013/05/20/behind-the-cover-story-michael-pollan-on-why-bacteria-arent-the-enemy/?action=click&module=Search&region=searchResults%230&version=&url=http%3A%2F%2Fquery.nytimes.com%2Fsearch%2Fsitesearch%2F%3Faction%3Dclick%26region%3DMasthead%26pgtype%3DHomepage%26module%3DSearchSubmit%26contentCollection%3DHomepage%26t%3Dqry393%23%2Ffermented%2Bfood%2F

Blog 8 - Continuation of Human Microbiome

I am going to be continuing this blog with the same article I used last week. Like I stated before, this article is very long, and very dense. It has a lot of information about personal experiences from the author, and many facts.

    I ended last weeks with the information about living communities and the microbes in a babies gut. When the author was in Boulder, he actually had a microbiologist, Catherine A. Lozupone, look at his Microbiome. As you may know, everyone has a different Microbiome. Usually people have a “normal” gut, and are very similar. But gut biomes can differ from various populations around the world. Scientists have conducted tests from thousands of different communities in and outside the U.S. The American Gut project will be able to uncover patterns between people’s lifestyles, diet, health, and various makeups of their bodies Microbiome.

 “microbially speaking: we share unusually high levels of prevotella for Americans. Our gut communities look more like those of rural Africans or Amerindians than like those of our neighbors.” Lozupone said.

The gut Microbiome is a very popular subject in scientific research. It is increasing in popularity, and most scientists are conducting more and more tests from around the world, to help them better understand what is actually going on in there.

This article is very well written. I like how the author writes about personal experiences he has with microbiologists, and the different things he has discovered with them. This article has so much useful information, and is one of the best articles I have read so far.

    

http://www.nytimes.com/2013/05/19/magazine/say-hello-to-the-100-trillion-bacteria-that-make-up-your-microbiome.html?pagewanted=all&action=click&module=Search&region=searchResults%230&version=&url=http%3A%2F%2Fquery.nytimes.com%2Fsearch%2Fsitesearch%2F%3Faction%3Dclick%26region%3DMasthead%26pgtype%3DHomepage%26module%3DSearchSubmit%26contentCollection%3DHomepage%26t%3Dqry116%23%2Fmicrobiome%2F&_r=0

Blog 7 - More about the Human Microbiome

     Since we have been doing a lot of recent work with the Human Microbiome, I searched New York Times and found an article called, “Say Hello to the 100 Trillion Bacteria That Make up Your Microbiome.” It was a very dense article with a ton of information.

     As you know, the human body is home to, well, 100 trillion microorganisms, that live on your skin, tongue, in your intestines, etc… and no two people are alike. When there is a disorder in your body (or “wrong” kind of microbes) can expose the body to obesity, viruses, and a range of diseases. Microbes in our system also play a role in maintaining our immune system, and are able to identify good organisms from the bad. Being able to study the different types of organisms in our body can help scientists come up with a cure for most diseases; but that day is still to come.

    The author of this article, Michael Pollan, wrote about his own experiences with the human Microbiome, and what he has learned. Did you know that microbial communities of couples sharing a home are similar? Or that having a dog increases the chance of blending everyone’s skin communities within a given household? He also went over how a baby’s gut community is highly colonized, versus being completely sterile in utero.  But a baby’s gut if far different from an adults; they lack an enzyme to digest carbohydrates in breast milk. It turns out that breast milk feeds a bacteria, Bifidobactrium infantis, which keeps the baby healthy, and nurturing the integrity of the baby’s intestines.

This is about half the information in this article. Like I said, it is very dense, and contains A TON of information. The main idea of the story is basically all about microbes that live among our bodies, ranging from adults and infants, and what those microbes do. I’ve learned quite a bit about the human Microbiome, but this contains so much information that I haven’t heard of before.

Since there was so much information, I will probably continue next week’s blog, with this article.

http://www.nytimes.com/2013/05/19/magazine/say-hello-to-the-100-trillion-bacteria-that-make-up-your-microbiome.html?pagewanted=all&action=click&module=Search&region=searchResults%230&version=&url=http%3A%2F%2Fquery.nytimes.com%2Fsearch%2Fsitesearch%2F%3Faction%3Dclick%26region%3DMasthead%26pgtype%3DHomepage%26module%3DSearchSubmit%26contentCollection%3DHomepage%26t%3Dqry116%23%2Fmicrobiome%2F

Blog 6 - Chernobyl Fungus

I was researching a few different extremophiles and came across the Chernobyl Fungus; also known as Radiotrophic fungus. These different types of fungi, obviously, can be found in the abandoned, radioactive city of Chernobyl. They aren’t you’re typical fungi. They can actually use radioactivity as an energy source to grow, make food, and reproduce.

Arturo Casadevall began studying this fungus about 5 years ago when he saw that a robot was sent into reactor 4 in Chernobyl, “and had returned with samples of black, melanin-rich fungi that were growing on the ruined reactor’s walls.” He immediately thought that these fungi could in fact be using the radiation as an energy source.

After Casadevalls peak of interest in this fungus, he performed a variety of tests with a few different types of fungi. They were exposed to different levels of radiation that were about 500 times higher than the radiation around us every day. The results proved that they do, in fact, use radiation as an energy source. The tested fungi grew faster when exposed to radiation.

"Just as the pigment chlorophyll converts sunlight into chemical energy that allows green plants to live and grow, our research suggests that melanin can use a different portion of the electromagnetic spectrum - ionizing radiation - to benefit the fungi containing it," said co-researcher Ekaterina Dadachova.

It is amazing to see that even in such an extreme environment, there are still microorganisms able to live and strive. I had no idea that certain microbes could live, and grow using radiation as their energy source.

Blog 5 - Microbes and Wine

     French winemaking uses a special concept known as “Terroir.” Such a mysterious word… and it will stay that way because there is no English definition. What we do know is that it is a combination of soil, geology, climate, and certain grape-growing practices. Terroir gives wine a very special taste. This special taste can make any wine taster identify where the wine originated. For years, United States vineyards have questioned the concept of Terroir, and recently, researchers have come to the conclusion that this distinct wine taste comes from bacteria that grows on the outside of the grape.

     

     These bacteria can affect the growth and health of the grapes. They are also incorporated in the mashing of the grapes. The different types of fungi that grow on the grape have yeast-like properties, and they help progress the fermentation. But, this is all just a theory. Researchers are not 100% for sure that this fungus is related to the Terroir.

    

      With advanced tools for studying microbes, a research team led by David A. Mills and Nicholas A. Bokulich sampled grapes from vineyards throughout California. They concluded that different microbes are related to different types of wine grapes. Different microbes are found in different vineyards as well. Some flourish in vineyards, while others don’t. They believe this is what gives the distinct flavor in each wine.

 Dr. Mills believes that there is a distinction between vineyards and microbes play a big role in this.

“On the other hand, he added, pinning the qualities of wine on bacteria and fungi may spoil that frisson of enchantment for some connoisseurs. “Many people don’t want this figured out,” he said, “because it demystifies the wonderful mystery of wine.”

I believe the authors main idea is very clear in this article. I knew microbes were involved in fermentation, but I had no idea different microbes flourished in different vineyards causing different tastes. 

http://www.nytimes.com/2013/11/26/science/microbes-may-explain-some-of-the-mysteries-of-terroir-and-wine.html?_r=0

Blog 4 - Red Tide

Since I recently did my essay, "A day in the life of a microbe,” about the Red Tide, I did a bit more research about it, and searched “Red Tide” on the New York Times webpage.

    Apparently, back in September of 2012, there were reports of a Red Tide pandemic in the Yangtze River of China. The water changed from the typical warm and brown, to a colder and rusty orange color. This was due to a “crimson current advancing alongside a stretch of untainted water.” The red tide is usually caused by an algae, and that’s what scientists thought this was; an algal bloom. The bacteria in the algae tend to feed off of warm and salty water and because of the climate change in China in 2012, the Red Tide algae blooms began to appear more and more. 

   Tests have been performed throughout the world to see what causes such a large spread. Reports of the Red Tide have come from Iran, Senegal, Russia, Ukraine, France and Turkey. Most reports in the United States tend to be from the Gulf of Mexico. The algae are a big concern. They can attack fish and can even be poisonous to humans (typically harmless, but can cause skin irritations). So it’s important to understand it, and see if these blooms are on the rise.

  

 This article wouldn't be very interesting to most people, especially if they haven’t learned much about the Red Tide. There would be a lot of questions about this article if there wasn't any prior research. Red Tide algae blooms can lead to high quantity aquatic life deaths, and is a big concern.

http://green.blogs.nytimes.com/2012/09/13/a-red-tide-epidemic/

Blog 3 - Bacteria in Your Car

When buying a used car, you don't just pay for a new vehicle, you also pay for all the bacteria and grossness that the previous owner left behind. Cars can be a bacteria breeding ground.

Back in 2012, Ford Motor Company conducted research with the University of Michigan to see really whats in your car. They mainly focused on employee owned Ford vehicles. 

Researchers tested 10 different areas in the car that included buttons, switches, shift knobs, handles, and especially the steering wheel. It was common to see that the steering wheel and area around the cup holders were home to most bacteria. These samples helped Dr. Blaise Boles to pinpoint where the most common place bacteria lived in a car, and the type of microorganisms that lived in those areas. 

Ford conducted this test in help of finding a paint to clean these places inside a vehicle, and are testing said product. It is used to not only sterilize the surface, but to also starve the microorganisms to stop microbial growth. Ford wants to use this paint in the cabins of future cars. 

But Ford only tested employee owned cars. There could be much more in older cars from the 90's and early 2000's. This was mentioned in the article and said, "the study doesn't distinguish between bacterial growth and the materials used in cars and trucks from other automakers." 

So once the paint product is finished, will it only be used on newer production Ford vehicles, or will the public be able to buy this product and paint it on their own cars? Everyone should care about the environment inside their vehicles, and maybe this is one big step towards that.

http://usnews.rankingsandreviews.com/cars-trucks/best-cars-blog/2012/11/Is_Your_Cars_Interior_a_Bacteria_Breeding_Ground/

Blog 2 - White Nose Syndrome

White Nose Syndrome (WNS) is a disease associated with the deaths of “at least 5.7 to 6.7 million North American Bats.” The disease is named after the distinctive fungal growth around the mouth and nose of bats. WNS was first discovered in the Schoharie County of New York in February 2006, but has grown to hundreds of caves all over the United States as of 2013.

“It is believed that Pseudogymnoascus destructans is the sole cause of the disease.” The white fungal growth around the bats mouth was analyzed microscopically, to find that it is a form of the Pseudogymnoascus destructans, which is the fungal infection associated with WNS.

White Nose Syndrome has greatly decreased bat populations in caves throughout North America. Some species of bats have already been listed as endangered. Bats play a big part in our environment. Without bats, “at least 2.4 million pounds of insects will go un-eaten and become a burden to farmers, possibly leading to crop damage.” – The United States Forest Service

North American bats are reaching a death toll of 7 million. Scientists are starting to find evidence about the fungal infection, and have come to conclusion that WNS fungus can survive in caves without the presence of bats.

Scientist, Hazel Barton (University of Akron professor), led the most recent research studies. One issue they found was that WNS not only lives around the muzzle, but also ears and wings, giving the bats “the appearance like they’ve been dunked in powdered sugar.”

The UA professors held a comparison of WNS to other cave dwelling relatives, and it was suggested that two closely related fungi share the same nutritional needs (found in cave soil) and are being transferred to the bats.

"Barton and her colleagues are zeroing in on when the fungus transferred from environment to bat and the consequences of the fungus' relentless ability to survive solely in caves, uninhabited by bats."

The article was very well written, but lacked more information about WNS itself, so I researched it a bit. Hopefully the scientists can figure out when the transfer of fungi happens, to help save millions of bats!

Article: http://www.sciencedaily.com/releases/2014/01/140129135108.htm

Wiki Page: http://en.wikipedia.org/wiki/White_nose_syndrome

Blog Assignment 1

Microbes Hitch a Ride on the Subway

       A Microbiologist from Colorado University, Norman Pace, has studied various types of microbes in all sorts of different places. He recently did a study of what kind of microbes live in the subways in New York. It was an experiment to see what people were breathing in the subway compared to what we breathe above ground. He performed these tests to see “if any of its invisible critters are cause for worry.”

Pace did various tests in multiple stations including Times Square, Grand Central, Union Square, Chambers Street, Bowling Green, and the IRT station. The tests that were conducted involved two samples of air about the volume of a persons breathe. Like I stated before, they were comparing the air below ground to air above ground. So they also sampled the air above.

The results were shocking. In the subway samples, each “contained almost one million bacteria” but tended to be the outdoor air. “Fungus loads are somewhat higher, but there’s also a lot of rotting wood, so that’s not so surprising”, Pace said. Five percent of the bacteria came from human skin. 

It was concluded that the air in the station had no cause for alarm or fear. Its just about the same air we breathe in any crowded outdoor space.

“We saw nothing unusual, certainly nothing threatening. At least, no more threatening than the people standing next to you on the platform.”

http://www.nytimes.com/2013/05/28/science/microbes-hitch-a-ride-on-the-subway.html?adxnnl=1&adxnnlx=1390503744-gojqfkrXQVQW8aLOy4Sw6Q&_r=0

Intro

I chose this course because I thought it would be an interesting science. It is also an FLC so I thought it was a good idea. My advisor also said that FLC's are a great combination of classes.

                                 National Geographic Photo of a Microbial Intestinal Bacteria
                               http://wordlesstech.com/2012/12/30/microbes-small-small-world/