(October is Here–Bloody, Ruddy, Muddy, and More!)

Aesthetics and microbes: check out the following snaps* to see microbial communities in nature!

blood fallsNational Science Foundation/Peter Rejcek Wikipedia commons

Antarctica’s Blood Falls, located at the tip of Taylor Glacier spurts a rusty curtain of briny water rich in iron-oxide. Autotrophic microbes (these fellows obtain energy from inorganic substances) live in this frigid, anaerobic environment. The microbes metabolize the ferrous and sulfate ions present in the water.

For more see:

1024px-Morning_Glory_Pool_(3678671791)Greg Willis Wikipedia commons

One of the quintessential Yellowstone National Park landmarks, Morning Glory pool awes millions of visitors each year. The hot spring contains beautiful, blue, gold, and purple tones thanks to the thermophilic* microbes that live in the 69.8 °C/157.6 °F waters. Unfortunately, the trash, coins, and other mementos tossed by tourists have blocked some of the thermal vents. This blockage lowers the temperature of the pool allowing brown/yellow bacteria that survive in cooler temperatures to thrive, diminishing MG’s original brilliant colors.

For more see:

1024px-Representatives_of_ceratioid_families Masaki Miya Wikipedia Commons

Female Anglerfish (Lophius piscatorius) have a ‘fishing rod’ apparatus on the top of their head. At the end of the rod is a short bulb-like structure, filled with bioluminescent bacteria (typically Vibrio or Photobacteria). The glowing bacteria lure prey: deep-sea dining made possible by microbes! Male anglerfish are much smaller and lack the rod/bait structure. In order to survive, the male anglerfish becomes a parasitic partner. The male latches onto a female anglerfish-permanently-his internal organs and eyeballs eventually atrophy as the male fuses to his mate!

For more see:

*snaps a Skope term meaning, an informative, short blog+photo note

**organisms that thrive in very hot temperatures (45-800C)




A Thank You with Some Fun Facts

 As of this weekend, 100 visitors have explored The Skope!* Thank you I am excited to continue sharing microbial/grad life updates and I hope you’ve enjoyed visiting the blog. To celebrate, I’ve created a short list of 100-themed fun facts:

100 the Centennial (ACADEMIA): The picture above is from the centennial logo of the University of British Columbia. Note the “00” shaped as the infinity symbol. Go Thunderbirds!

100 the Number (MATH): Did you know that 100 is a Leyland number? These numbers, named after mathematical theorist, Paul Leyland, follow the form:                                                                          x^y + y^x where X > 1, Y > 1                                                                                                                    26 + 62 = 100

100 the Gift (HISTORY): 100 years ago today, barrister Cecil Chubb bought Stonehenge as a present for his wife Mary. Chubb’s payment: £6,600! Stonehenge_(sun)

100 the Love Song (LITERATURE): TS Elliot publishes The Love Song of J. Alfred Prufrock and Other Poems 100 years ago… “Do I dare / Disturb the universe?”

100 the Microbiologist’s 1915 Discovery (SCIENCE): Clara Henriette Hasse published “Pseudomonas citri, the cause of citrus canker” in the Journal of Agricultural Research. Citrus canker causes leaf, fruit, and stem lesions on citrus trees. The infection may also cause citrus fruits to prematurely drop. Until 1915, no one knew what caused this disease. Ms. Hasse’s works helped save the citrus crops in the US.


Once again, 100 thank yous to all my readers! To get updates on new blog posts, follow The Skope (info on the right-hand sidebar).

*as of publication: 105 visitors, 271 views


BREATHE: Asthma and the Microbiota

(Antibiotics, Asthma, and an Idea)

Approximately 250,000 people die prematurely each year from asthma. Over the past century, asthma prevalence has continued to rise in developed countries. And prevalence is predicted to continue rising. According to the American Academy of Allergy, Asthma, and Immunology, the number of people living with asthma will likely reach 100 million by 2025. Recent studies have linked antibiotic use with allergic airway disease.* For Brett Finlay (University of British Columbia) the lightbulb moment occurred when his wife, a pediatrician, mentioned that children exposed to antibiotics as infants were more likely to develop asthma. Antibiotic treatment can result in massive changes in the gut microbiota community. Could our gut microbes impact asthma?


The Finlay Lab decided to conduct experiments examining the potential role of the gut microbiota on asthma susceptibility. The research, spearheaded by Shannon Russell, a UBC grad student, utilized an asthma mouse model. Russell found that mice treated with vancomycin, a commercial antibiotic, exhibited a decrease in gut microbes and increase in asthma severity. Changes in microbial composition were most pronounced in perinatal exposure (meaning the mama mice received antibiotics and the antibiotic exposure continued after birth). In contrast, the impact of vancomycin on the gut microbiota of adult mice was less severe. Furthermore, infant mice (but not adult mice!) exposed to vancomycin were significantly more susceptible to asthma.

According to the Finlay Lab, gut microbes have the greatest influence on immune development during a “critical window” from birth to three weeks of age in mice. Antibiotic treatment during this time frame impacts the development of the immune system and may contribute to the development of allergic diseases, including asthma.

The next step involves the development of better antibiotic and/or microbial therapies to treat bacterial infections without promoting asthma development. The gut-lung axis was (and is) a relatively new and unexplored field. I am excited to learn what my fellow lab mates discover next!

Sources + Additional Information:

* For a nice review, check out Noverr and Huffnagle’s “The ‘microflora hypothesis’ of allergic diseases” published in Clinical and Experimental Allergy:



(And not the kind that you receive from a University)

I think that the US should try the Celsius system. This may seem ironic since I recently wrote an article describing my preference for American English spelling. But I think temperature scales and spelling are quite different. Spelling is like an accent. Accents: Fun/quirky/exotic and reflective of heritage, but ultimately not a hindrance in communication. If I spell behavior and you spell behaviour—we would still understand each other perfectly. But if you said it is 250C outside, I (sadly) would still have to rely on Google to determine whether I need a sweater (770F, probably not). But here are a few reasons why I would prefer to use Celsius.

  1. Nearly the entire world uses Celsius! …with a few exceptions: Liberia, Palau, Belize*
  2. Inconvenience of conversions when traveling sans internet (probably not the strongest argument)
  3. It makes sense: 00 C for the freezing point of water and 1000C when water boils, versus 320 F and 2120 F, right?

thermometer Gringer: Wikipedia

The three most popular temperature scales are Celsius, Fahrenheit, and Kelvin. The last time I used all three was in a General Chemistry course, so I decided to learn a bit about their origins. Fahrenheit was developed by Daniel Gabriel Fahrenheit (1686-1736). Tragically, Fahrenheit’s parents died from ingesting poisonous mushrooms when Daniel was 15 years old. Fahrenheit moved to Dutch Republic and began pursuits in the natural science. His mercury thermometer and Fahrenheit temperature scale soon became widely utilized in Europe. The Celsius scale—a 1000 scale with the freezing and boiling point of water at either end—was developed by Anders Celsius. Celsius, a Swedish astronomer (1701-1744), was also was the first to connect the Earth’s magnetic field with the spectacular aurora borealis. The Kelvin system is mainly used in research. This system was developed by—you guessed it—a man named Lord Kelvin. William Thomas, Baron Kelvin of Largs (1824-1907) lived in Northern Ireland. In 1848 he wrote On an Absolute Thermometric Scale, which outlined the need for a scale that placed which absolute zero** at zero degrees. In Kelvin’s scale, the unit size between Kelvin and Celsius remained the same. During the 1800s, Europeans slowly adopted the Celsius scale. A switch further established when most countries adopted the metric system in the 1970s. So what do you think? Do you use Celsius or Fahrenheit? Should the world stick with one temperature setting? Submit comments below!

Sources + Additional Information: Encyclopedia Brittanica, Khandelwal and Agarwal’s The Fatal Recipe of Mushroom. SMU Medical Journal, 2014, and “On an Absolute Thermometric Scale” published on

*this is according to various maps on Reddit

**absolute zero-the hypothetical temperature in which there is no molecular movement, i.e. really really cold!



(So can I have Monday off?)

*I hope you had an amazing Labor/Labour Day Weekend. I had a blast at the Vancouver Aquarium. Here’s a blog post I wrote earlier this year after another long weekend. Hope you enjoy!*


During May, I spent most weekends trawling through Craigslist, Amsrental, and Kijiji to search for housing arrangements in Vancouver. I found a lovely suite and e-mailed the owner for more information. The landlord mentioned that showings would be unavailable during the Victoria Day weekend, but invited me to stop by the next weekend. Then, I received a second e-mail asking whether I—a grad student from the US—celebrated Memorial Day and would prefer to visit during a weekday. As I was living in the US, showings were a no-go, but the landlord’s thoughtful response piqued my interest in differences between Canadian and US holidays.

For starters, the US observes 11 federal holidays. Canada: 9-12 holidays*. Interesting…** Obvious dissimilarities include different dates for Independence Day/Canada Day and Thanksgiving. But there is also a financial difference. The US is the only developed country without (legally required) paid holidays. In contrast, European Union countries are required to give workers four weeks of paid holiday, reported USA Today. Hmmpf…Both Canadian and US citizens celebrate a long weekend in May: Memorial Day and Victoria Day weekend, respectively. Memorial Day honors armed forces members who died in service. Memorial Day was first observed in the late 1800s. Originally called Decoration Day, citizens decorated tombstones with flowers to honor fallen Civil War soldiers. Memorial Day became a federal holiday in 1971 during the Nixon Administration. Today, US citizens continue to place flowers and flags around the tombs of fallen heroes. Members of the armed forces are honored in special church services, town parades, and memorials at Arlington Cemetery and Capitol Hill. And like Victoria Day, this weekend also marks the unofficial start of summer. Victoria Day was first celebrated on the 24th of May 1835—the birthday of Queen Victoria. Later the date marked the birthday celebration of all current and future British Monarchs. And, in 1953, the Canadian government declared Monday, May 24 as a federal holiday (if May 24 didn’t fall on Monday, future holidays would take place the Monday preceding the 25th of May). I guess I will find ways to celebrate both holidays next year, even if I can’t take both Mondays off!

PS: yes, I did find housing!

Sources + Additional Information

*Apparently, there are 5 statutory Canadian holidays with additional paid holidays celebrated nationwide (or in the majority of the provinces). Canadians—help me out!

**If you’re curious, Argentina is the country with the most holidays: 19! In addition, there are many state holidays, as well. I spent six months studying in Entre Rios, Argentina and I really enjoyed experiencing the holiday-heavy culture.




Phil P Harris

(Or…Causation, Correlation, and Critters)

Michaeleen Doucleff recently posted about the gut microbiome in the NPR blog chronicling global health and development, “Goats and Soda: Stories of Life in a Changing World.” (If you haven’t visited “Goats and Soda” yet, check out the link below—G&S is one my favorites!) In How Modern Life Depletes Our Gut Microbes, Doucleff relates a New York University School of Medicine study characterizing the gut microbiome of the Yanomami tribe, a hunter-gatherer society that has lived for over 11,000 years in the Amazonian Mountains. Doucleff’s story begins in 2009, when Maria Gloria Dominguez-Bello, NYU colleagues, and a Venezuelan medical team first journeyed to the Venezuelan-Brazilian border to contact the Yanomami. Dominguez-Bello collected fecal samples from the tribe and used DNA sequencing to determine the Yanomami gut microbial profile. The Dominguez-Bello lab discovered that the Yanomami has roughly 50 percent more microbial diversity than the American gut. Or as Doucleff states, “Americans’ digestive tracts look like barren deserts compared with the lush, tropical rain forest found inside indigenous people.” As societies “Westernize”, communities lose microbial species. This loss of microbial diversity is typically accompanied by an increased incidence of autoimmune disorders and chronic diseases (think allergies and GI tract disorders). But are these facts related? Researchers don’t have a conclusive answer.

Indeed, microbiologists are still untangling the different factors that drive microbial diversity. Certainly dietary habits and antibiotic usage play an important role. Other researchers emphasize the hygiene hypothesis theory, noting that improved sanitation limit microbial diversity. Of course, Dominguez-Bello noted that these findings shouldn’t give license to romanticize the Yanomami lifestyle. The modern medical and hygiene advancements that may negatively impact microbial diversity have also enabled Western societies to enjoy a relatively healthy living and high life expectancy.

Dominguez-Bello’s study of modernization/urbanization and the gut microbiota is shared by her husband, Martin Blaser MD, the author of Missing Microbes: How the Overuse of Antibiotics Is Fueling Our Modern Plagues. A theme of the lively comments G&S section was the delineation between causation and correlation in microbiome research. Do our microbes drive specific autoimmune disorders (causation)? Or do the modern plagues arise from lifestyle/carcinogens/endocrine imbalance—resulting in subsequent microbial changes (correlation)?

20150906_170703 A KC Comic 🙂

Both the researcher and reader must distinguish between causation and correlation. And both Doucleff and Dominguez-Bello do an admirable job to avoid blurring of the two. When reading a journal/article, here are a few questions I ask to differentiate between cause and correlation:

  • Is there a mechanism/possible mechanism to suggest causation?
  • What are the limitations of the research?
  • Do other studies support the conclusions of the authors?
  • What further studies are necessary to demonstrate causation?

The best way to answer these questions is to be well-read in the field and/or have amazing research friends. As for now, I am excited to learn about the next developments in Dominguez-Bello’s project!

Sources + Additional Information


PASS THE MICROBIOME PLEASE: The Gut Microbiome and Energy Harvest

(A Tale of Two Mice)

Weight Loss and Gut Microbes: the (well-deserved!) reigning poster child of human microbiome research.

The story of how gut microbes impact host weight began at Washington University in Jeffrey Gordon’s Lab. In 2005, PNAS* published Ruth Ley’s “Obesity alters gut microbial ecology.” Ley, a post-doc in Gordon’s Lab, noted that certain gut microbes produce a variety of enzymes that enable the human host to extract calories from polysaccharides (think starch-rich foods, like potatoes). Without these microbes, humans are not able to digest many complex starches. Ergo, people predisposed to obesity may have über calorie-extracting microbes! Ley and members of Gordon’s Lab analyzed more than 5,000 gut bacterial genome sequences from the intestines of genetically obese mice (ob/ob mice) and their lean, wild-type siblings. The ob/ob mice eat excessively and develop obesity, high blood pressure, and increased insulin. Compared with their lean counterparts, ob/ob mice had a distinct microbiota, exhibiting a 50% decrease in Bacteroidetes abundance and a comparative increase in Firmicutes abundance.

OB:ob mice  Bigplankton @ en.wikipedia

(An ob/ob mouse and wild-type mouse)

Bacteria belonging to the Firmicutes or Bacteroidetes phylum* dominate both the mouse and human gut microbiota. Did the Firmicutes contribute to the ob/ob mouse’s efficient caloric/energy harvest and increased adiposity? Another post-doc, Peter J. Turnbaugh, further examined the ob/ob microbiome in a 2006 Nature paper entitled “An obesity-associated gut microbiome with increased capacity for energy harvest.” Using sequencing and comparative metagenomics, Turnbaugh found that the ob/ob microbiota contained higher levels of methanogenic microbes*** that increase bacterial fermentation efficiency, contributing to mouse adiposity. In addition, the ob/ob microbiome contained enriched DNA sequences of enzymes and proteins involved in microbial starch digestion. Next, the team transplanted either a wildtype or ob/ob microbiome in germ-free mice. Both groups of mice were maintained on the same diet. Two weeks after transplant, the mice that received the ob/ob microbiome had a higher abundance of Firmicutes and a greater increase of body fat percentage, compared with the mice that received the “normal” microbiome. Very cool. Perhaps future diets will include a serving of lean microbiome!

In 2013, I spent a summer interning at Turnbaugh’s Lab examining the role of antibiotics and diet on the gut microbiota. It was a wonderful experience that solidified my interest in pursuing microbiology for grad school. For more information, check out some of the amazing research at Jeff Gordon’s lab (WU), Ruth Ley’s Lab (Cornell), and Peter Turnbaugh’s lab (UCSF).

For a similarly awesome Microbiota and Obesity story: check out this image and the last link below

From:  Walker, Alan W., and Julian Parkhill. “Fighting obesity with bacteria.” Science341.6150 (2013): 1069-1070. Reprinted with permission from AAAS.


*Proceedings of the National Academy of Sciences of the United States of America. Established in 2007, PNAS Online publishes all PNAS articles from 1915 to the present. This is a great source for free, peer-reviewed articles.

** Remember King Philip Came Over for Ginger Snaps (Classification System: Kingdom, Phylum, Class, Order, Genus, Species)? Bacteriodetes: gram-negative, rod-shaped bacteria // Firmicutes: typically gram-positive and are usually rod-shaped or circular.

*** these archaea methanogens produce methane and derive energy from carbon dioxide.

Sources + Additional Information:



Screen Shot 2015-08-24 at 7.48.30 PM

(Tips from a Graduate Student Survival Guide)

My undergraduate Microbiology professor recently sent me a Science article entitled “A grad school survival guide.” The author, University of Colorado post-doc Andrew Gaudet, created a practical tutorial to help students navigate through the wonderful, hectic, challenging, and even tedious world of the graduate school. My favorite tip: “Start with the task you are least excited about, and do it right away.”

I don’t like to think of myself as a procrastinator; I make lists of things that need to get done; I set (mostly!) reasonable deadlines; I even keep a detailed calendar. But I struggle with starting the tasks. If I need to write a report, I first check my e-mail accounts, Facebook, weather station, and read a NY Times article (I need to stay up-to-date with my world, right?!). And before stopping by the lab, I obviously need to make a sandwich and check my laptop (see above). Now preparation is essential, but when preparation becomes procrastination any momentum grinds to a halt. Gaudet suggests tackling short-term tasks early in the morning, before checking e-mail or any procrastination-enforcing habit. Although I still check my e-mail fairly early, I’ve limited web-surfing until I’ve accomplished some of my daily tasks. And this new approach works for me! As Gaudet concludes, “Along the route to a Ph.D., rough seas can be navigated or avoided entirely. It takes many small successes, achieved day by day, to reach your long-term goals. So stay focused.”

Thanks for the good advice Andrew! And best luck in your research at UC!

Sources + Additional Information:

(Thanks for sharing RZ!)


ANTONIE VAN LEEUWENHOEK: The Father of Microbiology Part 2

(The boundaried life)

ˈɑntɔni vɑn ˈleːwənhuːk

I came across the following quote when researching Antonie Van Leeuwenhoek’s life. Any thoughts?

“Yet he always presents his results in a way which, despite the imperfections of his language and his lack of scientific education, is a model for all other workers. He never confuses his facts with his speculations. When recording facts he invariably says “I have observed …”, but when giving his interpretations he prefaces them with “but I imagine …” or “I figure to myself …” Few scientific workers — or so it seems to me — have had so clear a conception of the boundary between observation and theory, fact and fancy, the concrete and the abstract” 


Protistologist to the Medical Research Council, London

Foreign Member of the R. Accademia dei Lincei, Rome

Sometime Fellow of Trinity College, Cambridge

Imagine unveiling the miniature world, making discoveries that would fuel the study of microbiology, virology, microscopy, and even physics. In scientific research speculations/opinions are considered a double-edged sword. On one hand, speculations reveal the potential importance and possible future research; on the other hand, speculations can result in fatal errors when accepted as truths. Delineating between truth and thought prove blurry in every field of thinking. Perhaps the best way to honor both “facts and fancy” might be, like Leeuwenhoek, to establish clear boundaries between the two.

PS-Check out some of AvL’s original illustrations below:







(A) Sheep semen (B) bacillus bacteria (from the human mouth) (C) corn weevil

For more information see:,




(Or how an alien benefits from Microsoft Word)

My first inclination that pursuing doctoral studies would be an alien experience came from an e-mail that thanked me for applying to the University of British Columbia’s Microbiology and Immunology Doctoral Programme. ProgramME? Now I’ve traveled (oops travelled) to Canada, England, and Scotland on educational tours. My family drove to Quebec City and vacationed on Prince Edward Island. Many of our books (hello Cuthberts, Pip, and Bennets!) were printed in the UK, so I am familiar with the British system of spelling. Still, the extra “me” reminded me that I had excitedly accepted an international graduate program. And for someone who can’t remember whether canceled has one or two Ls (L in the American system and LL in the British system), the thought of remembering alternative spelling (or is it speling…haha, jk!) was enough to produce a twinge of anxiety. Of course, there are handy rules in place. Nearly every word ending (and pronounced!) ER is spelled RE by Canadians. The British system favors (or favours?) LL, while the American system uses L. The British system utilizes stately Ss, whereas Americans usually prefer the more eccentric Zs. But, as everyone knows, the English language treats rules more like working hypotheses rather than scientific laws. For example, we write counseLLor (B) versus counseLor (A) but look at fulfiL (B) versus fulfiLL (A). And why write glamOUR (BB) to describe a glamOrous (BB) dress? Strange…

Nevertheless, Microsoft Word provides spelling salvation in the form of international spell check. For those who are curious click Systems Preferences>Spelling>British system. I suppose that when I submit my thesis or write my first assignment or article I will change language preferences. But for now, I think, I will stick with my homeland spelling just for a while longer.