Friday, June 8, 2012


Molecular Dialogues with the Microbes Inside Us  ~A talk by Dr. Karen Guillemin

There is a new understanding that based off of the 10 trillion cells that compose is ~25,000 genes and in getting close to knowing all of our genes, it has been discovered that the gastrointestinal tract has 10^14 cells (~1,000 species) which is roughly 2,500,000 genes. This number easily dwarfs that of the human genome.

Since Antoni Van Leeuwenhoek (A Dutch merchant) developed his town lenses for a hand-held microscope, there have been various ideas as to how we view the body and assess the host-microbe relationship.

The Germ Theory of Disease is one such view. Louis Pasteur and Robert Koch both said that diseases were able to spread because they contained spreadable agents within the microbes. This ideology gave microbes a bad name and blamed them for diseases that we couldn't see and therefore had difficulty treating. Around WWII there was the implementation of penicillin that paved the way for other antibiotics to fight against harmful pathogens

In her talk, Dr. Guillemin poses 3 main questions:
1) How did they get there?
2) How stable are gut microbial communities?
3) Can changes in the microbe community cause diseases?

In answer to the first question: How do they get there, we looked at birthing methods and the microbes that are associated with each. When the mother gave birth vaginally, the baby showed more microbes from that region of the body. If it was a cesarean section, the baby exhibited more of the mother's skin microbes. There is also the matter that when mothers nurse their babies, the breast milk contains sugars that the human body cannot break down. This promotes the symbiotic relationship between humans and our gut microbes.

How stable are gut microbial communities? This is a flexing question since there have been a vast number of changes in human ecology so we have altered the microbes that live inside us. We have made a shift to being more sterile, our food is more processed, and the change in birthing routes (now 1/3 of the country's births are cesarean sections). This shift has greatly cut down on the microbial biodiversity that has helped us historically. It is yet to be determined what the consequences to this are but there are some theories, which leads us to question 3:

Can changes in the microbe community cause diseases? The Hygiene Hypothesis (David Strachan 1989) says that if we are cleaner and avoid microbes, we are putting ourselves at a greater risk for developing auto-immune diseases. The Disappearing Microbiota Hypothesis (Blaser and Falkow 2009) says that the microbes in our bodies are more than just a random occurrence and we are losing the microorganisms that have been important historically. This second hypothesis questions whether or not the altered microbiota in diseases are a cause or consequence of this.

Dr. Guillemin described the work that was being done with Zebrafish to determine if altered microbiota in diseases were the cause or consequence of the loss of microbes. Zebrafish are ideal model animals since they are similar to humans in the inter workings and they are easy to examine since they are transparent and their genes are easy to manipulate. This image shows that the introduction of microbes into zebrafish greatly reduces, if not completely stopping the gut motility found in the fish. An experiment was done to see if the bacteria that was introduced caused inflammation of the gut in a sterile zebrafish. First, they started with a mutant fish strain who exhibited not gut motility, was defective in gut clearing and thus, had inflamed guts. To test whether or not this was a direct result of the bacteria introduced, the bacteria was extracted (gut motility visible, reduced inflammation) and then reintroduced into the system (no gut motility and inflammation had returned). This experiment showed that the inflammation was due to the microbiota and that the gut microbial community in the mutant fish caused transmissible intestinal inflammation - microbes drive the disease.

So what does that mean?

Many advances are being made, but we are still unsure of a great number of the inter workings of the microbial community within us. Some things that Dr. Guillemin suggests we do to promote our body's  microbial community are to nurture our gut microbes by using antibiotics judiciously and avoiding over processed foods, and to nurture environmental microbes through supporting the responsible use of antibiotics in agriculture and animal husbandry as well as supporting efforts to reduce human impacts on the environment.

Tuesday, June 5, 2012

Molecular Dialogues of the Microbes Inside Us

         Professor Guillemin’s talk at the Microbes of the Modern World lectures inspired awe in listeners about the microbes within us.  While many people think of pathogens that cause diseases in people when they hear the word “microbes”, Professor Guillemin’s work with the Human Microbiome Program illustrated how integral microbes are for the function of our body.  She opened her lecture by providing some context for the influence that microbes have on the human body: there are more cells of bacteria in the gastrointestinal tract than there are cells in the entire body.
           The Human Microbiome Program works to survey the micro-organisms throughout the human body.  They look note the differences in composition of these microbes at different locations throughout the body.  Data by the HMP has found that people have completely distinctive microbial communities, as distinctive as fingerprints.  This individuality raises several questions for further research:
            -    What factors determine microbial composition?
            -    How stable is the gut microbial community (is it stable over a person’s lifetime?
                 Across generations?)
            -    Can changes in microbial communities cause disease?

Graph showing microbial composition of babies based on
method of birth
            A human baby is sterile or without microbes until it is born.  As you can see from the graph, the composition of a baby’s microbes is determined by the method by which it is delivered.  A baby that was born vaginally has microbes similar to that of its mother’s vagina whereas a baby born via cesarean section has a microbial composition similar to the skin of the mother as well as the skin of the doctors and nurses present in the operating room.  Additionally, it has been found that microbial communities change as a diet changes.  It has even been found that breast milk contains sugars that specifically support growth of particular microbes.  These data suggest that microbial composition is determined by a person’s exposure to people, environments and even diet.

           Another important issue to examine was whether altered microbiota communities cause disease or are merely a consequence of it.  Through the use of model organisms, such as zebrafish, Guillemin can look for possible sources of causation.  Characteristic shifts in communities have already been associated with specific diseases.  This could have important implications as disease could soon be seen as changes in microbial communities.

Zebrafish: the model organism (source)

             One important feature that makes the model organism zebrafish prime for research on microbes is that they can be reared sterile and then have microbes introduced into their systems.   This allows researchers to determine whether differential microbial communities cause symptoms, such as inflammation, or are a consequence of these symptoms.  Guillemin’s lab looked at a mutant fish that had difficulty clearing their gut of old microbes from their food also tended to have an inflamed gut and increased concentrations of immune cells.  By using germ-free fish, they found that inflammation was actually caused by the different microbiota.  This data suggests that different microbiota might actually drive disease or cause transmissible intestinal inflammation.  Learning about the important impact that microbiota can have on human health inspires us to learn to nurture our internal microbes as well as the microbes found in the environments we live in. 

Sources cited:

 Guillemin, Karen. "Molecular Dialogues with the Microbes inside Us." Microbes and the Modern World: From the Globe to the Gut. Lillis Business Complex, Eugene, OR. 29 May 2012. Lecture.

Saving Our Planet's Biodiversity By Reducing Our Carbon Footprint

 Human activities have caused our planet’s biodiversity to decline at unprecedented rates. Global climate change remains a great threat to Earth’s biodiversity, and carbon dioxide emissions from human activities are the primary cause of climate change. For these reasons, it is important to consider the carbon footprint of human activities.  Essentially, the carbon footprint calculates the amount of carbon dioxide emitted by human activities, such as driving and flying.  Fossil fuel combustion is the primary source of carbon dioxide emissions into the atmosphere. To provide some perspective, using one gallon of fuel in your car produces 19 pounds of carbon dioxide. Given that the average American drives 12,000 miles each year with a 20 mile per gallon vehicle, each American emits 12,000 pounds of carbon dioxide each year from driving alone.

Image source: (
The image above shows the breakdown of an average person’s carbon footprint, with gas, oil, and coal making up 15% of the typical person’s carbon footprint.
Image source: (
As you can see from this image, fossil fuel combustion contributes 82% of the carbon dioxide emitted on this planet. Reducing fossil fuel combustion is necessary to reduce our individual carbon footprint. Since fossil fuel combustion comprises a large part of our carbon footprint, we must continue to develop affordable alternative transportation options.
Video source: (
 The video above shows the combined volume of carbon dioxide emitted in just one minute by China and the United States, compared to the rest of the world. As you can see, the United States and China carbon dioxide emission values are equivalent to 400 meters, which is equal to the height of the Empire State building.

 These staggering statistics show that within one day, humans emit incredible amounts of greenhouse gases from burning fossil fuels. Why is reducing our carbon footprint important? Carbon dioxide emissions from the burning of fossil fuels has been implicated as the main cause of global climate change, and many organisms will not be able to survive the current rate of climate change. Specifically, increased global temperatures have been identified as a primary factor in the decline of amphibians. Since amphibians typically occupy narrow ranges with specific temperature and moisture conditions, they are greatly threatened by global climate change. One study found that climate change also puts amphibians at greater risk for infection by pathogens, (Rohr et al, 2010).

 Reducing our carbon footprint is also crucial for preserving arctic life, which is under great threat due to climate change. Both marine and terrestrial life in Arctic regions will not be able to adapt to shrinking ice caps and warming ocean waters. For example, the National Wildlife Federation website ( explains that the ice- free period in the Hudson Bay has increased by 20 days in the past 20 years. This increased ice- free period has reduced polar bear’s seal hunting season by three weeks. With this narrower hunting range, polar bear weights and reproduction rates have declined. Therefore, any efforts to conserve our planet’s biodiversity must begin at reducing our carbon footprint. By reducing our carbon footprint, we will decrease the current rate of climate change, and in turn, help preserve our planet’s biodiversity.
 Image source: (

 What can we do to reduce our carbon footprint? In a report released by the Metropolitan Policy Program at Brookings in 2008 (, large urban regions with high annual-passenger miles of rail transit had lower per-capita carbon footprints than urban regions with less rail transit available. Therefore, large cities must invest in rail transit to reduce the carbon footprint from transportation. However, implementing mass rail transit requires government involvement and would incur high costs. Individuals can help reduce their carbon footprint by making small changes to their daily lives. When possible, we should use bicycles to travel to school, work, or other places within a reasonable distance. We can also utilize public transportation when commuting to work each day. In cities without reliable public transportation or bike routes, forming car pools is an option that would help reduce the carbon footprint from driving. All these personal lifestyle changes are cheap to implement and are relatively easy to do. These changes would help conserve our planet’s biodiversity by reducing the amount of carbon dioxide emissions from fossil fuel burning.

 In addition to the changes mentioned above, the development and widespread use of energy sources that don’t burn fossil fuels will be required to reduce our carbon footprint. A recent recent New York times article explained that electric cars which use clean sources of electricity, such as hydroelectricity, can reduce the carbon footprint by almost 50% of today’s most efficient gasoline-based vehicles. This study did not take into account the carbon footprint from manufacturing and changing electric car batteries. To reduce carbon footprint emissions from our vehicles, it is also important to consider how manufacturing electric batteries affects the environment. Electric cars aren’t widely available and are often more expensive than traditional vehicles. Furthermore, electric vehicles have limited ranges and to extend the range, electric vehicles also have gasoline engines. Therefore, electric vehicles can reduce our carbon footprint greatly, but until their cost and range are equivalent to gas-powered vehicles, we will continue to rely on fossil fuels for transportation. This highlights the need to continue our investment into cleaner transportation, because our current carbon dioxide emissions from vehicles will cause continued global climate change and great biodiversity threat.

 Image source : (

 We also need to consider how airline travel affects our carbon footprint.  A cross country flight from New York City to San Francisco and back emits approximately 5,000 pounds of greenhouse gas emissions for each passenger. Since two cross-country flights emits almost half as many greenhouse gases as driving 12,000 miles a year does, flying makes up a significant portion of our carbon footprint. We must cut the number of flights taken each year, and if possible, use high-speed rail or buses to make those cross-country trips in order to significantly reduce our carbon footprint.

 To protect the planet’s biodiversity, we need to address the main causes of biodiversity loss. The carbon footprint is important to consider when tackling this daunting task. Since the carbon footprint measures carbon dioxide emissions from human activities, we can determine which activities emit the most greenhouse gases. With greenhouse gases being the primary cause of global climate change, reducing our greenhouse emissions will help reduce the rate of climate change as well as reduce the loss of biodiversity. From using public transportation to developing electric vehicles, we can make the necessary changes to reduce our carbon footprint. However, we must be motivated to make these changes and begin today, because if we maintain our current carbon footprint, we will not be able to conserve this planet’s biodiversity.

Works Cited

Molnar P., Derocher A., Klanjscek T., Lewis M. Predicting Climate Change Impacts On Polar Bear Litter Size. 2011. Nat Commun. doi: 10.1038/ ncomms1183. 

Rohr JR, Raffel TR. Linking Global Climate Change and Temperature Variability to Widespread Amphibian Declines Putatively Caused By Disease. 2010. Proc Natl Acad Sci USA. 107(18): 8269-74.


Microbes and the Modern World: Karen Guillemin

    The last talk in the series of talks was presented by Dr. Karen Guillemin. She focused most of her talk about the microorganisms that live with us. 
   Dr. Guillemin started off the lecture talking about the history and current study human-microbe interactions. She talked about how the current study of human-microbe interactions has allowed us to shed a new light on who we are as individuals. And due to the advancements in DNA sequencing techniques, we are able to get an idea of the microbes on and inside our own body as well as a visualization of our own genome. She mentioned the Human Microbiome Project and their goal to answer the question, ‘what kinds of microbes are present on the human body?’. So far, they have uncovered the fact that different microbes reside at different parts of the body and that there is a lot of variability of residential microbes as you go from one person to the next. She focused her main topic of discussion on our residential gut microbes, which is something she has been personally experimenting with for some time now. She began by posing a few questions such as ‘how do they get there?’ and ‘can changes in the microbial communities cause disease?’. Some ways that microbes get to us is through our diet and our genetic makeup. She talked about how birth was our initial inoculation event and how depending on the way our mothers gave birth to us is a crucial cause of what microbes are present. Another inoculation is nursing; studies have shown that mother’s milk actually contains certain microbes that are beneficial to the baby’s health. Onto her actual case study, she talked about using Zebrafish as a model organism due to its transparency and having a digestive system similar to our own. Dr. Guillemin is very well known for her work with germ-free organisms such as the Zebrafish. Germ-free organisms are a good way to help deduce the function of a particular microbe by inoculating a single or a group of microorganisms at one time. 

Biodiversity Loss: A Major Driver of Ecosystem Change -Professor David Hooper

When I first heard that we could get extra credit for our biology class by attending an ecology lecture by Professor David Hooper I thought, why wouldn’t I go? This is the first professional in the field of biology I have ever heard of with my same last name!

Professor Hooper began his lecture by posing the question, “Do changes in diversity effect ecosystem processes?”  He then further broke this question down into three more questions: 1) What are the magnitudes of effects on processes relative to other environmental changes? 2) What are the effects on things that people care about? 3) How are ecosystems actually changing?

To explain the answer to his first question, he went into details about his recently published paper, “A global synthesis reveals biodiversity loss as a major driver of ecosystem change”. This paper was a meta analysis of 192 studies containing 574 experiments all following a specific criteria. Hooper looked at productivity vs. species richness (SR) of primary producers and decomposition vs. SR of primary producers as well as vs. consumers. Overall he found that with species loss productivity decreases and these effects on productivity were comparable to the effects of other environmental changes.  When looking at decomposition it was found that a decrease in litter diversity did not show significant change in decomposition while a change in consumer levels did show a change. All of these results showed high variability.

His second question was explained by looking at different kinds of ecosystem services, excluding cultural services. In the end, this question had mixed results because ecosystem services are hard to quantify and mean different things to different people.

Hooper concluded with answering his third question and saying that there is a need for further research on a larger scale so that we will better be able to look at and understand the connection between biodiversity effects and ecosystem changes in the real world. 

Monday, June 4, 2012

Microbes and the Modern World
From the Globe to the Gut
Dr. Karen Guillemin

Dr. Guillemin, an associate professor in biology at the University of Oregon gave an interesting lecture discussing microbes in the human body. She told the story microbes in the body by using paintings as a real life representation of what is going on in the body. Through her research and the Human Microbio project, scientists are trying to describe the microbial ecosystem in the body. In this project, they are trying to figure out what factors determine community composition, how stable these guy microbial communities are, and can change the microbial community cause disease? Another question scientists are trying to address is the hygiene hypothesis or the disappearing microbiota hypothesis. Right now there is a correlation but scientists must get causation before it is accepted in the science community. By using zebra fish in the laboratory, they are trying to answer these questions.
         By studying the gut communities in these zebra fish you can predict what is happening in the human gut. In the wild type zebra fish, there is a normal gut community where food is moved by a peristaltic waves. The mutant fish's gut community did not exist and there was also an inflammation and lack of peristaltic waves. From this, scientists are able to see the effects of microbes in the guts on the function of the gut. This is represented by a continuing flow in the relationship between the gut health, the gut environment, and the gut community.
         Microbes that are found in your gut, like the ones in this study are determined from a variety of factors stemming from when you are first born. What microbes you start off with depend on if you have a natural birth or if you are born by a c-section. After this first moment on earth, everything you encounter effects your microbial make up, including the food we eat. However, the food we eat is becoming increasingly more and more sterile and processed. This is causing a decrease in the natural microbes that you would normally encounter in non processed food.
         Dr. Guillemin finishes the lecture with suggestions on how to nurture your gut microbes. She suggests that you use antibiotics sparingly and when you only really need them, avoid food that your grandmothers microbes wouldn't recognize, and to nurture your environmental microbes by supporting responsible use of antibiotics in agriculture and animal husbandry.


Grebes. University of Oregon. Retrieved June 2, 2012.

Professor David Hooper - Effects of Diversity on Ecosystem Processes: Does it Matter?

Professor Hooper measuring plant productivity

 Professor David Hooper, a professor at Western Washington University, has been receiving a lot of attention, including his most recent article in Nature, for his unique perspective on the relationship between levels of biodiversity and ecosystem services.  What is unique about this aspect of thinking is that many people think that reduced ecosystem services have negative impacts on species, reducing levels of biodiversity, not the other way around. 


           order to further explore this perspective, Professor Hooper and his team at Western Washington University have performed an enormous meta-analysis, looking at 192 studies, which include 574 experiments.  In particular, they examined studies that dealt with a manipulation of species richness, randomized data and looked at a response to a change in ecosystem process rates.  With this wealth of information, Professor Hooper began to evaluate the relationship.  They looked at and analyzed data for several conditions to attempt to illustrate the relevance of this relationship such as plant productivity and species richness of primary producers. When examining this data, they found that with more species lost there were greater impacts on the rates of productivity, as seen the graph below:

This figure not only illustrates that loss of species has a great impact on the ecosystem process of productivity, but it makes a point to emphasize that it is not an negligible impact.  Many people assume that the magnitude of this sort of effects are greatly outshone by those that we are familiar with, such as global warming, invasive species, etc. But, as you can see from the Y-axis on the right of this graph, the resulting loss of productivity due to species loss is actually comparable to many of these other more familiar effects on ecosystem services. 
            While Professor Hooper and his team were definitely concerned with being able to illustrate this relationship, what they really wanted to know was whether it mattered, as evidenced by the title of his presentation.  Hooper said that there were three questions that he wanted to answer with this study with his last question having the most resonance: In terms of how ecosystems are actually changing, does it matter?  In order to really answer this question Professor Hooper emphasized the need to look at how ecosystems are changing.  Professor Hooper suggests that the best way to determine this is to look at the link between ecosystem functions and services.  While his data does suggest that how ecosystems are changing does matter in terms of the effects of species richness, there needs to be much more future research.  In order to evaluate the relevance of this study and to determine whether the species loss patterns are reflected in real life, there needs to be a large increase in the scale of these experiments and a better way to replicate species loss.  It will be exciting to see what Professor Hooper elucidates next. 


Effects  of Diversity on Ecosystem Processes: Does it matter?-David Hooper

           David Hooper, a professor at Western Washington University, has been crucial in development of the field of ecology and a key component in linking ecosystem processes with bio diversity. In his lecture "Effects of Diversity on Ecosystem Processes", Hooper talks about his publication "A global synthesis reveals biodiversity loss as a major driver of ecosystem change". In his paper, Hooper and his colleagues used a method known as "broad analysis" or "meta-meta" analysis to look at resources in the science community and to compile an overall result of what is going on in an ecosystem. In this analysis, they looked at production vs species richness of primary producers, decomposition vs species richness of primary producers, decomposition vs species richness of consumers, and other environmental factors. They looked at 192 studies, 574 experiment, and 1417 effects size that all used randomized design to ensure that there was no criticism of the studies. Overall what they found was that species loss was comparable to other environmental factors.

               One of the most interesting things in the talk by Hooper was his explanation for why there were such wide error percentages, which in class caused a lot of students to second guess the legitimacy of the paper. He explained that this was due to the fact that when you are doing a meta-meta analysis there will be a wide range such as a range of a loss of 60% - to a gain of 70% because it depends on the species that make up each monoculture and what is in that culture and the diversity and make up will directly effect those results. 
             After finishing up the talk on "A global synthesis reveals biodiversity loss as a major driver of ecosystem change" he switched gears to another paper of his that is coming out in the next few weeks. This paper is a review paper that looks at types of diversity changes such as changes in number of types of "SPUs" and the effects of the absence of entire groups. 
         Hooper finishes with three main things that he thinks need to change to help in the advancement of biodiversity on ecosystem research. These were 1. there needs to be a better link between ecosystem functions and ecosystem services, 2. Expand our focus, and 3. Improve predictions. Right now in the linking processes and services, scientists are only looking at primary or decomposers, but he suggests that we need to look at the bigger picture and look at the two together. He suggests that we expand our focus by looking at patters of loss and by changing the scales of our experiments. When looking at patters of loss, we should look at interactions with environmental change, how much diversity is at risk, links between global and local species loss, and species richness vs functional traits of particular species. Finally, when changing the scales of experiments, he suggests looking at how change in landscape effect ecosystem services. With these suggestions, Hooper feels that the possibilities in advancement in this field are endless and invites students to really dive deep into the field of microbes and ecology.