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Hiring a Lab Technician

7 Feb

I’m a Fatboy Slim fan, and when I decided to write today’s post, “Praise You” started playing in my head.  Besides the fact that I need to update my music taste, it reminded me that I want to thank all my faithful followers out there for waiting around for me to post again.

It’s been ages (2 years to the day) since I’ve posted and I salute you both.

Many things have changed since I was blogging last… I’m now the proud SciMom to two little rugrats, and a tenure-track faculty member at Wazzu.  [I feel somehow obligated to assert the obvious fact here that all opinions given in this blog are my own and have absolutely nothing to do with my university.]

That’s right folks, 2 virtual petri dishes that crawl and drool and snot all over the place, AND all the responsibilities of a brand-new, wet-behind-the-ears ass prof (assistant professor, for those of you confused about the abbreviation); I’m just a glutton for punishment.

This has given me a new-found sense of juxtaposition: freedom, weighed down by grant-writing; imagination, mired in the realities of funding priorities; and an awesome new job, potentially debunked at tenure-review time.

I, therefore, chose to attempt to squeeze into my painstakingly time-managed work-day schedule some time for fun-writing (aka, blogging).  The shape and form and overall thrust of this blog will largely remain the same – Microbes do, in fact, still rule the world, and I will continue to extoll their virtues.  However, I hope to also cover science and science events more broadly and may even share the odd job posting. (a clear transition into…)

With my very first blog as a new tenure-track faculty, I will shamelessly let you all know that I need to hire a lab technician.  I need someone with experience in soil microbiology and molecular biology, cultivation-dependent and independent techniques.  The pay is not particularly great to start and I can’t cover relocation costs, but the boss is usually pretty cool and she’s super enthusiastic about what she does.   And you should know that Eastern Washington/northern Idaho is not the big city, but rather the outdoor-enthusiast’s playland.  So, for the full job description and details, contact her directly.


Dogs, Dust, and the Hygiene Hypothesis

7 Feb Since I’m still only getting about 3 or 4 hours of sleep at night, extracurricular reading for this blog has to be uber-interesting to maintain my attention long enough to keep me from falling asleep halfway through the abstract.  Not to say that anything microbial isn’t particularly interesting, but the bar has been set a little higher now that I’m a SciMom, and baby girl likes to eat… a lot.

So, in looking for something exceptionally interesting to blog about this week, I stumbled on the perfect storm for today’s paper, which piqued my interest for several reasons that may or may not be obvious you folks out in readerland.   First, I just had a baby a few months ago and find myself continuously thinking I need to do more research on this or that which will affect the baby’s health and wellbeing.  Second, I have “indoor pets”, namely several German Shepherds (see the shamelessly cute photo below) and two cats.  Third, I was diagnosed with allergy-induced asthma when I was about 9 years old and have struggled with it ever since (you may be wondering at this point, why on earth I would have so many indoor pets if I have allergic asthma… just call me a glutton for punishment, but I love my dogs).

The unifying theme of the paper, however, and overarching interest for me is, of course, due to the very cool and omnipresent impacts of microbial ecology.

Exactly how microbial ecology plays a role in a study on prenatal and early childhood exposure to indoor pets and how that affects immunoglobulin E may not be overtly obvious, so let me explain.

What does hygiene have to do with it?

First, you need a cursory understanding of something called the “hygiene hypothesis”.  It’s pretty huge in the health news these days so I wouldn’t be surprised if you’re at least vaguely familiar with the concept.  Essentially, it’s the idea expressed beautifully by Rob Dunn in Eating off the floor: How clean living is bad for you.  The basic idea is that the more of our little microscopic friends that we are exposed to early in life, the healthier we are overall due to stimulation of our immune systems in a way that allows natural development and response to true pathogens.  Early exposure to a range of microbes is thought to essentially “teach” our immune systems what is good, safe, or at least not a threat, versus those organisms that can really make us sick and should be eliminated.

The slightly longer than 5-second rule...

If we live in an environment where everything is sterile (at least as much as possible), our air is filtered, antimicrobials are everywhere, antibiotics are over-prescribed, and we aren’t exposed to microbes and parasites, then our immune systems may begin to overreact to anything and everything regardless of the potential harm it might cause us. This would explain the rise in autoimmune disorders and asthma, some even include eczema and hay fever.

As cool as all that is, it is only a hypothesis at the moment, which means we need (lots) more evidence (a.k.a. data) to be able to assert these ideas as a theory, much less a fact (of course we all know that in Science, reaching the status of “theory” is as good as it gets… only the media and snopes assert “facts”).  And it’s even a fairly vague hypothesis at that.  We’re not sure which types of microbes we need to be exposed to, how many, at what times, and precisely which aspects of our immune system will or won’t be affected.

The word for the day: Pets

There is currently a lot of work ongoing around the globe to get at some of these different aspects of the hygiene hypothesis and hopefully begin to provide us with the data we need to assert that, in fact, microbial exposure is a good thing for the development of the human immune system.  One such study came out in 2010  in the Journal of Allergy and Clinical Immunology which compared the microbial communities in dust of homes with and without pets.  They proved what all us pet-owners already know, that the dust of homes with pets supported a much more diverse microbial population than the homes without pets.

Dust mite

In this most recent paper, Suzanne Havstad and her colleagues took this idea one step further.  They set out set out to provide more details of the dynamic interplay between these pet-based dust microbial populations and the human immune system.  This particular puzzle piece involved testing immunoglobulin E (IgE) levels in the blood of young children in response to their exposure, or lack thereof, to indoor pets.

What is IgE, anyway?

Admittedly, the various components of human immune system (and vertebrate biology, for that matter) are well outside the scope of my own training and expertise.  I will therefore refer you to the following article on Immunoglobulin E and this medical article on pediatric asthma (you’ll find the bits on the hygiene hypothesis in under “Pathophysiology”).

In a  nutshell, IgE is part of our immune system which is triggered by allergens and parasites in your environment, including worms.  It causes inflammation that helps your body defend against intruders and keep you healthy.  However, it’s also thought to play a very significant role in pediatric asthma since blood IgE levels in asthma sufferers are typically much higher than non-asthmatics.  Essentially, some people’s immune systems overreact to things like dust, pollen, dander, etc, which leads to excessive production of IgE which in turn causes inflammation of tissues in lungs and bronchial tubes and asthma (not being able to breathe) is the result.

What Suzanne Havstad and her colleagues were able to conclusively prove was that children who were exposed to indoor pets in utero or in their early years had significantly lower IgE levels than those who weren’t exposed to pets.  The more diverse microbial community of the homes with pets must be interacting with the children’s immune systems and fostering the lower IgE levels, right?  It’s certainly possible and makes all the sense in the world to somebody like me.

However, just because [A (pets) = B (more diverse dust  microbial communities)] and [A (pets) = C (lower IgE levels)], doesn’t necessarily in this case mean that B =C as well.  There could be any number of other factors for children in the homes with indoor pets that may or may not have been measured, such as lifestyle, diet, exercise, and exposure to other allergens or toxins in their environment.  These other factors could also be influencing IgE levels.

However, what makes this study more compelling is that they also found an effect of the child’s mode of delivery:  vaginally versus Cesarean section.   The reason I say that this makes the study more compelling is because it’s been found that infants delivered vaginally have an entirely different microbiome (indigenous microbial community) than those delivered by C-section.  This lends some weight to the idea that microbial populations influence IgE levels.

What does it all mean?

This study seems to doubly lend support to the idea than early microbial exposure impacts human immune

A shamelessly cute German Shepherd puppy.

response, particularly via IgE levels.   Indoor pets can clearly increase the diversity and abundance of the microbial populations of your household dust (not a fact, that in and of itself, I really want to spend a lot of time thinking about) and exposure to that dust may actually be a good thing, in moderation (i.e. we probably shouldn’t spoon-feed the dust to anybody), for children’s developing immune systems.  Take home message: every kid needs a dog, or a cat, or both, or to at least get a little dirty every now and then… which means my little girl has got this covered!
Havstad, S., Wegienka, G., Zoratti, E., Lynch, S., Boushey, H., Nicholas, C., Ownby, D., & Johnson, C. (2011). Effect of prenatal indoor pet exposure on the trajectory of total IgE levels in early childhood Journal of Allergy and Clinical Immunology, 128 (4), 880-8850000 DOI: 10.1016/j.jaci.2011.06.039

In the spirit of the day…

14 Feb

Despite the fact that I really don’t celebrate VD (Valentine’s Day, in case you were thinking something else), I thought I would show a little love, share a warm-fuzzy, and re-post this from Suzanne Kennedy (clearly, a woman after my own heart) at the MoBio Blog,  The Culture Dish.

Oh how do I love thee? Let me count the ways…

Show some LOVE for Environmental Microbiology

Do you love your work? Does nothing make you happier than a day out in the field collecting soil from the rainforest floor, in a boat collecting Vibrio contaminated water from Puget Sound, traipsing the forest looking for animal droppings from wild birds in Venezuela, or aboard the Alvin collecting biofilms from deep sea floor hydrothermal vents?

It’s important to love your work and fortunately for us, there is so much to love about microbiology and the environment. But to find out what is best about working in this field, I asked the question to several of my scientist friends:  What do you love about your work? Why do you study environmental microbiology and what is it that makes it the best field of work?

And below are some of the best responses. Some are my own, but most are responses I received from people who study some of the most unusual samples from the most extreme environments in the world.  I think you will agree that environmental microbiology provides experiences unlike any other field. Let us know your reasons for loving your work!

14 Reasons to Love Environmental Microbiology:

1. You get to play outside in the mud, snow, water or clouds (see picture at end of article).

2. There is virtually an unlimited number of research projects to choose from. “Microbiologist William B. Whitman, estimates the number of bacteria in the world to be five million trillion trillion. That’s a five with 30 zeroes after it. Look at it this way. If each bacterium were a penny, the stack would reach a trillion light years.”

3. Your research will have an impact on everything living on the planet, humans, animals, and plants. Basically all the Kingdoms benefit from what you do.

4. You have the opportunity to visit exotic and remote locations.  

Graduate student Rick Davis explains, 

“I think I’ve been really lucky with the places I get to study– I got to go to Samoa, Hawaii, and Yellowstone this year!”

He also added reason number 5: 

5.  Environmental microbiologists are more laid back and generally more collaborative than competitive, which allows for greater progress and more fun at conferences!

John Mackay, a molecular biologist and director of business development at the plant diagnostic company, Linnaeus, tells me:

6. You can cruise around the seas for months, sequence a bit of sea water and write the whole lot off on your research grant!

7. You can work on things you can eat or drink – I recommend wine and truffles!

8. When you find new species (almost a given!), you can name them after yourself.

 New discoveries are also what motivates Charlie Lee from the University of Waikato, a Postdoctoral researcher in microbial ecology studying the Dry Valleys of Antarctica. He echoes the sentiment that discovery is almost a guarantee:

9. Most systems we look at are relatively poorly understood, and it’s always exciting to discover something for the first time.

 Tom Niederberger, a Postdoctoral researcher in marine biosciences at the University of Delaware, has more to add:

10. The international travel is a great reward. The world is your playground as microbes have colonized basically all habitats on earth, and it’s great to travel around sampling not only the microbes, but new cultures/food/travel etc. and not being chained to the lab and pipette. Also the international collaborations and conferences also are great.

11. But I think what is most important is that microbes in the environment are essential not only for the health of the planet (e.g. global nutrient cycling / global climate change) but they are also intimately linked to the healthy functioning of our bodies. i.e. the are really important!

12. Also,there is the excitement of the unknown. Most of the organisms cannot be cultured and we know nothing about them…I think this is great motivation and it will keep you busy, and there are always new problems to solve and new questions to ask.

All excellent points!

And from a molecular biologist from Colorado State University (who wished to remain anonymous) come two excellent points I hadn’t considered:

13. Extremists don’t kidnap environmental microbiologists. Actually, they give them back.
If you get tenure, who’s going to boot you out?  Exxon?

Did I mention that environmental microbiologists are funny?

Microbes Make it Snow

1 Feb

This post was chosen as an Editor's Selection for ResearchBlogging.orgThe recent snow and ice, and deeper snow, and even more ice, across much of the U.S. over the past few weeks have finally inspired me to put together my first post for the new year.  You’re probably wondering how on earth microbes have anything to do with the 3 feet of snow you had to dig your car out from under last week…  

…but hear me out.

Blowing in the wind

I have two “believe it or not” statements for today: First, believe it or not, microbes are ubiquitous in the Earth’s atmosphere (Bowers et al. 2009, and others).  “Ubiquitous” is a fantastic word that simply means “absolutely everywhere” and it’s especially true with microbes.  As a soil microbiologist, I immediately think of soils and sediments all over the globe and the wide array of fungi and bacteria that keep the planet green (and purple and red and brown), and it makes sense because there are so many things to eat in soils.  There’s a never-ending supply of nutrients from dead and decaying plants, worms, insects, other microbes, and even weathering rocks.  But I also know that out in the open ocean microbes are abundant and provide the foundation for the food chain, not to mention nutrient cycling and overall marine ecosystem health.  We’ve known these things for quite some time now (hence, my “microbe-centric” view of life). Our Microbial Planet Poster

What doesn’t always make sense to a terrestrial biologist is that microbes are also extremely abundant in the air around us, above and beyond our reach, floating in the breeze and being carried thousands of miles on trans-oceanic trade winds.   It’s true, though, and for years we assumed that these microbes must be in a sort of hibernation mode, because there’s nothing to eat, harsh conditions often including extreme dryness, cold temperatures and powerful UV radiation from the sun.  More recently, however,  we’ve begun to understand that only a portion of these airborne microbes are hibernating, while others remain active, usually bound in soil particles or cloud droplets (Sattler et al. 2001).  And as long as these little guys are metabolically active, they have the potential to make changes to their environment, even in the atmosphere.

Ice, Ice, Baby (sorry, I couldn’t help myself)

Which leads me to my second “believe it or not” statement for the day:  many of those atmospheric microbes have been found to nucleate ice (Bauer et al. 2003).  What I mean by “nucleate ice” is that they can serve as the starting point for ice crystals to begin to form.   What makes this really cool (pardon the pun) is that ice-nucleating microbes have been found to make specific proteins on the surface of their cells which catalyze the formation of ice crystals at relatively high temperatures.  This action not only allows the crystals to form outside the microbe, rather than inside where ice crystals would damage cellular membranes and kill the microbe, but the formation of these crystals also releases very small amounts of heat energy, keeping the microbe that much safer from freezing. 

Commercial snow-seeding material.

Commercially available snow-seeder.

You might have heard about these guys (indirectly) before if you’ve ever heard of “cloud seeding.”  There’s a commercially available freeze-dried preparation of ice-nucleating bacteria that many ski resorts will shoot up into the clouds to help encourage snowfall.  A slightly less well-known practice is the application of “ice-minus” bacteria to reduce crop loss due to frost.  In that case, growers have taken advantage of specific mutant bacteria which lack the genes for the ice-nucleating protein and spray these bacteria across the foliar surfaces so that ice won’t form as easily.  The idea here is that ice-nucleating bacteria are very commonly found on plant surfaces, and can lead to frost damage.  But those lacking the gene (called “ice-minus”) when applied to the plants, outcompete the natural bacteria, and reduce the formation of frost on plant surfaces.   

Atmospheric Microbes = Snow

How bacteria make up snowflakes.

Bacteria and snowflakes.

But these ice-nucleating bacteria exist all over the world, in the soil and in the air around us and may be affecting more than just the ski slopes and strawberries.  A very interesting study by a group of scientists out at the University of Colorado in Boulder recently looked specifically at ice-nucleating bacteria and how microbial abundances in the atmosphere may alter atmospheric conditions (Bowers, et al 2009).   In order to address this question, they took a number of air samples from the Storm Peak Laboratory at the top of Mt. Werner near Steamboat Springs, CO.  Their air samples contained over 640 different bacterial species (via genetic sequence), but their data indicated they did not even begin to sample the full diversity of the airborne microbial community.  Despite variable weather conditions during sampling, the total airborne microbial numbers remained stable and didn’t change throughout the sampling period.  However, with increasing relative humidity, there was a significant increase in ice-nucleating bacteria.  They found that the abundance of ice-nucleating bacteria was significantly greater in cloudy air samples, than in clear (or non-cloudy) air samples.  They even suggested that some bacteria may be able to respond to favorable (humid and cloudy) conditions and adjust their concentrations of ice-nucleating proteins, consequently increasing the ice-nucleation potential of these species.

Take-home message…

So, what does all this have to do with the massive downfall of snow and ice this season?  Well, as much as I love to blame global warming for more extreme weather events, we don’t have to connect a whole lot of dots to be able to believe that atmospheric microorganisms may be playing a role as well. 

The more people we have on the planet, the greater population densities become, and the more disturbance we cause to land surfaces, the more soil, dust, particulate matter, bacteria and fungi rise into the atmosphere and interact with our weather patterns.  Much the same way that cloud seeding works, it seems our activities down here are affecting the number of microbes and consequently cloud formation (bioprecipitation, if you will) up there.


Bauer, H., Giebl, H., Hitzenberger, R., Kasper-Geibl, A., Reischl, G. Zibuschka, F., and H. Puxbaum. 2003.  Airborne bacteria as cloud condensation nuclei.  Journal of Geophysical Research, 108:4658.

ResearchBlogging.orgBowers, R., Lauber, C., Wiedinmyer, C., Hamady, M., Hallar, A., Fall, R., Knight, R., & Fierer, N. (2009). Characterization of Airborne Microbial Communities at a High-Elevation Site and Their Potential To Act as Atmospheric Ice Nuclei Applied and Environmental Microbiology, 75 (15): 5121-5130 DOI: 10.1128/AEM.00447-09


Griffin, D.W. 2004.  Terrestrial microorganisms at an altitude of 20,000 m in Earth’s atmosphere. Aerobiologia, 20:135-140.

Sattler, B., Puxbaum, H., and R. Psenner. 2001.  Bacterial growth in super-cooled cloud droplets.  Geophysical Research Letters, 28:239-242.

Some yogurt each day keeps the doctor away

8 Oct

Health Benefits of Yogurt

There’s a great deal of debate these days about the sometimes wild and often wondrous health claims touted by the probiotics movement.  These special beneficial bacteria (mostly lactic acid bacteria like those found in yogurt, and available now it the convenient pill or capsule form) are claimed to not only cure everything including digestive disorders,  irritable bowel syndrome, pediatric asthma and allergies, but are also said to be capable of preventing a wide variety of problems including acne, eczema, vaginitis, halitosis, and even cancer.  Those skeptics (realists?) among us realize this is most likely impossible. 

I, of all people, would love to believe that just hand-full of species of beneficial bacteria, when ingested on a regular basis, can make the sick well, heal our wounds, lower our blood-pressure, and bolster our immune systems, but that’s the stuff of science-fiction fantasy and all rather outlandish. 

Or is it?

I posted a few weeks ago about a clinical trial using lactic acid bacteria (like those found in yogurt) to help mice stave off flu symptoms and found I had unwittingly placed myself on the side of the argument with the “snake-oil salesmen” and moneymakers (aka, commercial probiotics salespeople).  I do love to play devil’s advocate on occasion, so I began looking into the subject a bit more… where do all these various and sundry health claims come from? Are skilled marketing strategies simply playing on the human desire for a cure-all, a fountain of youth, or is there some seed of legitimacy at the base of it?

Probiotic Bacteria

On my quest for truth, I found first, the report by the American Academy of Microbiology, “Probiotic Microbes: The Scientific Basis”… a must-read for any truth-seeker on this subject.  However, since the time it was put together (November 2005), the myriad of health claims being made in the media (as well as the backlash against) has vastly expanded, and science did not have a grasp of precisely how this all worked within the human body. 

Which brings us to my second discovery in my quest: a truly seminal research study which (finally!) very clearly indicates how probiotics modulate human cellular pathways to achieve several varied, and perhaps unexpected, health benefits.  The article by van Baarlen and colleagues (full citation below) was actually published online in the Proceedings of the National Academy of Sciences the same week I made my original post on yogurt bacteria (Sept 7, 2010).

The study involved seven healthy, non-smoking adult human volunteers and the transcriptional responses (meaning, which genes were being actively expressed) of their stomach mucosa to consumption of live cells of Lactobacillus acidophilus, L. casei, L. rhamnosus, or a placebo control.    Every volunteer was exposed to each of the four treatments, with a two week break, or rest period, between treatments. 

The first discovery was that the gene expression profile of each of the volunteers was considerably different, regardless of treatment.  Of course, this reflects the fact that we are each individuals and our health and well-being is a sum of our genetic make-up, our environment and experiences.  But the implications are clear when we consider the conflicting results of many of the probiotic clinical trials.  Natural variation of genetic expression between individuals is high enough to mask the observed clinical effects in some people while not in others, especially when combined with the different effects of each bacterial species. 

This brings me to the second major discovery: the fact that each of the bacterial species tested had significantly different effects on the mucosal gene expression profile (GEP) of each volunteer.  By this, I simply mean the following:

  • L. acidophilus elicited changes in genes involved in stimulating and regulating immune response (both innate and acquired: increased interferon and antibodies), and hormonal regulation of water and ion homeostasis, increased tissue growth and wound healing, and metabolism regulation.
  • L. casei lead to gene expression regulating the balance between innate and acquired immune response, as well as metabolism regulation and regulation of hormones involved in blood pressure.
  • L. rhamnosus caused expression of genes involved in wound repair and healing, innate immune response (interferon), and ion homeostasis.

All three bacteria stimulated responses involved in innate immune response, while L. casei also caused modulation (balance) of the innate vs. acquired immune response.  The authors noted that the response to each species of bacteria was markedly different, and that these differences could extend as far as the growth stage of the bacteria in the probiotics preparation.  What this means is that every probiotics product on the shelf is not created equal; the species, even variety, is important, and the methods used to cultivate and preserve the organisms may be important as well (i.e. live cultures are best).

Because of the fact that the technology used in the approach for this study is fairly new, we actually don’t have a lot of human mucosal gene transcription profiles to compare these types of data against (in other words, we can’t see how these data align with other data from similar studies, because there are not yet any other similar studies).  So, my first thought was something along the lines of, “How do we know the same GEP might not be elicited if somebody ate food, or anything for that matter?”   The authors expected questions like that and therefore compared their data with data from GEPs of human cell lines exposed to various compounds.  The results of this comparison were quite interesting:

  • L. acidophilus had similar effects to drugs for hypertension, convulsions, and inflammation.
  • L. casei caused had similar effects to drugs used to treat muscle hypertension, water retention, and inflammation.
  • L. rhamnosus elicited effects similar to drugs used against protozoan infections and to amplify bowel movements.

So, not only could they directly measure certain genes in the human stomach mucosa responding to the probiotics in a way that suggested modulation of the immune system (amongst other things) but the response was actually similar to the effects of drugs engineered to treat and modulate that very thing.  Fascinating! 

This study is obviously not the end-all and be-all of probiotics work, but it’s a huge piece of the puzzle in terms of why probiotic clinical trials have yielded such conflicting results, and particularly how probiotics modulate the immune system in a variety of ways and against a variety of afflictions.  It certainly supports the mouse-flu study I blogged a few weeks ago.  The authors conclude,

 “We anticipate that responsiveness to probiotics is not only determined by characteristics of the consumed bacterial strain but also by genetic background, resident microbiota, diet, and lifestyle.  This study could, therefore, be among the first steps to investigate the interplay between microbiota, probiotics, or other nutritional supplements and human genetics tow personalized nutrition.”

To me, this says that if you already have a healthy immune system, you work-out and eat right, get enough rest and all that, you might or might not notice a difference from taking a probiotic.  However, if you’re immune system is already compromised, you regularly drink, smoke, are largely sedentary, and stay up all night doing who-knows-what… if you opt for a cup of yogurt instead of a Twinkie, you just might thank yourself in the morning (and now we have the data to prove it!).

van Baarlen P, Troost F, van der Meer C, Hooiveld G, Boekschoten M, Brummer RJ, & Kleerebezem M (2010). Microbes and Health Sackler Colloquium: Human mucosal in vivo transcriptome responses to three lactobacilli indicate how probiotics may modulate human cellular pathways. Proceedings of the National Academy of Sciences of the United States of America PMID: 20823239

Yogurt bacteria knock back influenza

9 Sep

Homemade yogurt

I recently mastered the art of yogurt-making…  or, I guess I  could say it more precisely: I learned how to manipulate a commercially available consortium of lactic acid bacteria (LAB) to make yogurt for me using common, household materials in my very own kitchen.  As a soil microbiologist, I love running these little experiments at home – the do-it-yourself mad-scientist approach to homemaking.

According to all the “make your own yogurt at home” websites, blogs, and YouTube videos, the number of live organisms in the homemade stuff is substantially higher than in store-bought stuff, which means it confers much greater probiotic benefits; unfortunately, I couldn’t find any original research to back this claim.  In my futile attempts to find more information on the proven health benefits of homemade yogurt (I need something to convince my friends and family to eat the stuff now that I’ve made loads of it), I came across a pretty cool study that I decided to share; it’s not exactly environmental microbiology, but a very cool case of microbial/human ecology (and particularly relevant as flu season approaches).

By way of introduction to the subject…

The most common bacteria in store-bought yogurt are Lactobacillus delbrueckii and Streptococcus salivarius; these little guys and their cohorts earn the label “live active cultures” in the fine-print on the side of the yogurt container.  Some commercial yogurts may also contain certain bifidobacteria, and you can even purchase a “yogurt starter” which is a mixture of two or three lactobacilli, along with the Streptoccocus and a bifiobacterium.  These LAB function to convert the lactose (milk sugar) into lactic acid via fermentation, and voila! Yogurt!

But it just so happens that many of these types of organisms (LAB) naturally live in the human gut (not to mention a variety of other locations on and in our bodies) and help us digest our food.  So, if for any reason a person’s gut microflora get perturbed (let’s say by a dose of antibiotics for that ragweed-induced sinus infection), then we can safely and effectively re-introduce these good bacteria to our digestive tract by eating yogurt and virtually eliminate the upset stomach and diarrhea that might have resulted otherwise.

This all seems pretty straightforward, and science has had a good hold on this aspect of probiotics for quite some time now.  However, a much more interesting aspect of this story has arisen recently, regarding the human immune system.

“Emerging evidence from recent clinical and animal studies supports the notion that probiotic lactobacilli, especially some selected strains, can modify host innate and acquired immune responses by which they can protect against respiratory infections.” – Kawase, et al. (2010)

The flu study

The authors administered live cells of either Lactobacillus rhamnosus or Lactobacillus gasseri (also found in yogurt and closely related to the other LAB mentioned earlier) to a group of 13 mice (one group for each species of bacteria, plus a control group = 39 mice), once each day for 19 days.  On day 14, the mice were also inoculated with the mouse-version of the H1N1 flu virus.  From that point on, the mice were visually monitored for flu symptoms, and the level of virus in the lungs of the mice was measured at the end of the experiment (I’ll spare you the gory details of how they performed that last part).

What they found was that all the mice seemed just exactly the same until 2 days after they had received the H1N1 virus.  The effects of the probiotics were not evident until the control mice, who had not received either of the LAB, began to fall ill.

By 6 days after infection with the virus, the control mice were displaying clinical symptoms of the flu (headache, fever, glued to the couch with a blanket sipping chicken soup, etc), while the mice on the probiotics were looking significantly better and acting healthy (jogging, biking, playing horseshoes, you get the picture).

But seriously, not only did the treated mice look better and seem to human observation to be feeling better, but the level of virus in their lungs at the end of the experiment was significantly lower (less than half) compared to  those mice who had not received either of the lactic acid bacterial treatments.  The researchers also found pathological changes in the lining of the bronchial tubes in control mice that did not exist in the treated mice.  There appeared to be no difference in the protective effects of each species of bacteria; both conferred disease resistance equally.

I have to admit I was skeptical at first read, but with a little more digging, I found these results were supported (albeit indirectly) by in vivo (Harata et al. 2009) as well as in vitro work with immunocompromised model animals (Yasui et al. 2004).  These studies demonstrated altered immune response in terms of cytokine and IgA production and increased survival rate, all in response to LAB probiotics, but the mechanism remains unclear.  How does it work?  We don’t really know yet; it just does.

Of course, these aren’t humans we’re talking about, and quite a few studies have attempted to reproduce a similar effect in children and infants, to decrease allergies and/or asthma and the results are a mixed bag.  There are so many additional factors that could confound work with human subjects, though… at least with the mice, you know exactly what they eat, when, how long they sleep, what they do all day, and it seems to me that you could never know all that with human subjects, no matter what they say on that questionnaire.  Just another reason I prefer to do my science with microbes.

In a nutshell

It seems certain species of lactic acid bacteria like those we find in yogurt, when ingested, have beneficial effects on disease resistance in mice, and potentially in humans as well.  I suspect this work by Kawase et al. could be just the tiniest tip of a very fascinating iceberg.

In the meantime I’ll be watching (and taking notes) on how many of my home-made yogurt connoisseurs come down with the flu this year.  Eat up!

ResearchBlogging.orgKawase, M., He, F., Kubota, A., Harata, G., & Hiramatsu, M. (2010). Oral administration of lactobacilli from human intestinal tract protects mice against influenza virus infection Letters in Applied Microbiology DOI: 10.1111/j.1472-765X.2010.02849.x

Harata, G., He, F., Kawase, M., Hosono, A., Takahashi, K. and Kaminogawa, S. (2009) Differentiated implication of Lactobacillus GG and L. gasseri TMC0356 to immune responses of murine Peyer’s patch. Microbiol Immunol 53, 475–480.

Yasui, H., Kiyoshima, J. and Hori, T. (2004) Reduction of influenza virus titer and protection against influenza virus infection in infant mice fed Lactobacillus casei Shirota. ClinDiagn Lab Immunol 11, 675–679.

The newest bacterium: Part 1

30 Jun

During my blog-writing hiatus, some interesting science has made the news, science that not only affects my field in particular, but the world at large.  The buzz about the creation of a “synthetic cell” has received a great deal of attention and stirred a lot of questions.  I’ve had my own questions about it and have formed a few opinions about the way the authors as well as the media in general has handled the issue.  I therefore will begin my blog anew with a few posts on the newest advance to come from Craig Venter’s research group.

What I’m interested in for the sake of discussion here is specifically:

1.) The research article from whence the hubbub began (how’d they do it?);

2.) How it fits into the field of environmental microbiology (and microbial ecology)

Science or semantics?

So, in an attempt to simply understand what this was really all about, I began by delving into the original research article in Science which came out on their Sciencexpress website on the 20th of May 2010, entitled “Creation of a Bacterial Cell Controlled by a Chemically Synthesized Genome.” 

First off, what struck me was that the title of the article distinguishes the actual, peer-reviewed scientific work from the terms the popular media and news press were using… “synthetic cell” or even “synthetic life”.  This undoubtedly originated from Dr. Craig Venter himself in several (non-peer-reviewed) interviews in which he stated, “We call it the first synthetic cell…” and this is the terminology used on the J. Craig Venter Institute  (JCVI) homepage.  However, I feel this is misleading and that a little clarification might be in order. 

The original cell itself was, in fact, not synthetic, in the most basic sense of the term.  It was a organic, all-natural (not man-made) bacterium growing on a Petri dish in the lab, an organism by the name of Mycoplasma capricolum, which causes respiratory diseases, mastitis and severe arthritis (in goats). 

The scientists did not manufacture the lipids, proteins, and other components of this life form, nor did they create it “from scratch” or “from four bottles of chemicals” as the popular media might have you believe.  Venter and his cohorts synthesized genetic material similar to another closely related organism and inserted into an already living M. capricolum cell.   Once this genetic material was inserted into a living cell, the cell then made copies of that synthetic genome, grew, and divided into new cells directed by the man-made synthetic genetic code.

A true scientific feat, no doubt, but not exactly the way it’s been spun.    

You might consider this experiment something like  a brain transplant in a human (bacterial nucleoid = human brain).  The scientists didn’t create the body, the lungs, liver, heart, skin, spleen or any other organs of this living thing; they simply created a new brain, built to spec off a very closely-related person’s real, live brain, and put it into a body from which they had removed the previous brain.  A truly amazing and admirable scientific advance, but they didn’t create a synthetic human being from chemicals in the lab (on a dark and stormy night with a timely strike of lightning).

Of all the articles and interviews I’ve seen, I actually thought Nicholas Wade  used more accurate terminology and gave this advance a more realistic billing than most others in his article in the NYT.  One subject the NYT article brought up is the fact that the bacterium used in these experiments is not actually suitable for most other biotechnology applications.  So, what is a Mycoplasma and why use it in this type of research? 

In future posts, I address this question and begin to look at the more technical aspects of the research itself.


Gibson, D.G. et al. (2010) Creation of a bacterial cell controlled by a chemically synthesized genome.  Science, 329 (5987): 52-56.  DOI: 10.1126/science.1190719