Tag Archives: Bacteria

What are you doing to the microbes in your gut?



Lactobacillus casei, a microbe found in dairy products, the human intestine and mouth. Source: Flickr, user: ajc1

There are a hundred trillion cells in our body. You might think that most of the cells are human, but in fact, 90% of these cells are tiny microorganisms like bacteria that we can’t see with the naked eye! But where do these microbes come from, and what are they doing in our body?


Source: Wikimedia Commons, user: BruceBlaus

All mammals, including humans, are usually born free of bacteria and other microbes. However, shortly after birth, babies become colonized by microbes that come from their parents, the food they eat, and the environment. The colonization of our gut by microbes continues throughout our entire lifespan. The population of microbes in our gut tends to become more complex as we get older and start consuming solid food.

Now that we know a bit about how we obtain these microbes, how are they affecting us?

 Most of us reading this blog have “Westernized” or modern lifestyles, where we have access to clean water, processed food, modern medicine, and hygiene. This does not mean that our environment is completely sterile, but as it turns out, the gut microbe population is less diverse in people in Westernized populations compared to rural populations.

 So why is this important?

Lower diversity of microbes in our gut is associated with autoimmune diseases like Crohn’s disease and irritable bowel syndrome, as well as conditions like multiple sclerosis and autism. It may also explain why there is a higher prevalence of conditions like asthma and allergies in modern society.

 Watch the following video which showcases our interview with Dr. Laura Parfrey, a researcher in the Departments of Botany and Zoology at UBC, to find out more about how our lifestyle influences our gut, and more importantly, what we can do to make our gut microbes more diverse.


Source: own work

Dr. Parfrey recently found that the diversity of gut microbes differs between Westernized populations and rural populations. She specifically looked at eukaryotic microbes, which are essentially all the microbes that aren’t bacteria, and found that the Western population had a much less diverse set of microbes! This may help explain the increasing prevalence of autoimmune diseases and allergies in modern society. According to Dr. Parfrey, there is still a lot that we still don’t know about how microbes affect our health, and she explains further research questions and why she finds her research interesting, in the following podcast:


Source: own work

So, there are lots of microbes in our body, especially the gut, and they’re affecting our health more than we’ve thought previously! In order to keep our gut microbes healthy and diverse, people can avoid overemphasizing hygiene with their kids; and as for adults, people can incorporate more diverse sources of food into their diets, especially diverse sources of complex carbohydrates.


sick? eat s###!

Recently, Scientists and Researching physician have made poop pills a viable therapy against C. Difficile infections.

Frozen pills of fecal matter, ready for ingestion. - NPR/ Hohmann Lab

Frozen pills of fecal matter, ready for ingestion. – NPR/ Hohmann Lab

Why would anyone in their right mind want to ingest pills filled with poop? according to the lead researcher, Dr. Elizabeth Hohmann, it’s a big step from the previous methods of enemas and nose drip-tubes, which were accident-prone, especially “if people gagged and vomited, they could inhale fecal matter. “

Yikes. Why are people taking such grotesque (if not extreme) methods for treatment? what exactly is a C. difficile infection, and why is it so difficult to treat?

Clostridium difficile  is a type of bacteria that is known to cause “opportunistic infections”, or infections when the host is able to be infected easily, usually with the host being in a weakened/compromised state; in this case, most of the cases of C. difficile infections are caused by the lack of other, more benign bacteria colonizing the intestines, usually due to antibiotic treatment. This is akin to introducing wolf packs onto a sheep farm, where there are no competitors/predators for the wolves. As a result, the wolves prosper, at great cost to the sheep and the sheep farmer – a fitting metaphor for both the person infected by C. difficile , and the physician treating it, since C. difficile infections are especially antibiotic-resistant, and are prone to recurrent (i.e: multiple and returning) infections.

How C.difficile spreads- Wikipedia/CDC

The purpose of undertaking fecal transplants is to re-populate the patient’s colon and intestines with benign/helpful bacteria, thereby out-competing the harmful C.difficile. In an extension to the wolves/farmers metaphor, this would be akin to introducing more farm workers, scaring away the wolf pack and ensuring the prosperity of the farm.

Of course, the draw-back to this form of therapy is the “ick-factor”, effective though it may be.  This is why scientists have been working on a synthetic version of the bacteria flora populating our gut- dubbed appropriately, “rePOOPulate”. Research is still on-going  in the field of bacteria flora colonizing our gut; hopefully, one day someone can invent a form of therapy with all of the benefits of faecal transplants, and none of the “ick-factor”.

YouTube Preview Image  Source:Mary Greely Medical Centre, Via YouTube

– James L.

The bugs in your guts are making you fat.

Generally when we think “bacteria” and “guts”, we think of nasty things like food poisoning or the stomach flu. But in reality, there are large amount of bacteria living in our lower digestive system – what scientists call the Gut Microflora. In fact, some recent research has shown that the bacteria living in our guts aren’t simply enjoying a tenant-landlord relationship; in fact, they may actively contribute to our overall health. A good example of this is the much-hyped “probiotics” recently being promoted as the new “superfood” essential to successful diets. As Yogurt companies have been advertising left and right,   “an exclusive probiotic culture … has been shown to survive passage through the digestive tract in sufficient amounts for Activia to help regulate the digestive system”. But is there any truth to this?

Some research has indicated that certain species of bacteria may contribute to the overall efficiency of energy extraction and affect overall levels of host obesity;  and in fact, studies in mice have shown that mice with differing levels of obesity has different compositions in their gut microflora, showing quite the correlation between bacterial colonies in the gut and obesity. This begs the question, Would changing the bacteria help make you skinnier?

 Scientific American-Volume 310, Issue 6. "How Gut Bacteria Help Make Us Fat and Thin"

Scientific American-Volume 310, Issue 6.
“How Gut Bacteria Help Make Us Fat and Thin”










To make a long and complicated answer short, We don’t know.  Though there has been trials done confirming the short-term effects on things related to obesity, so far no study has proven effective, as the gut microflora is a complicated subject with many facets to watch.  That being said, There are current studies in the works, so keep an (critical) eye on your news feed, and feel free to eat all the yogurt you’d like.

– James L.




Who said you can’t see bright stars in the deep ocean?


Euprymna scolopes by MattiasOrmestad

A photo of a Bobtail squid,  Euprymna scolopes, performing bioluminescence. It’s underside is brightly lit by its symbiotic bacteria V.fischeri. Photo by Mattias Ornestad on kahikai.org

Euprymna scolopes, commonly known as the Bobtail squids, are found around the Hawaiian Islands. Additionally, they’re about 4.5cm and has one other amazing fact: they have an indirect ability to perform bioluminescence, which is the production or emission of light by living organisms.  To be exact, the Bobtail squids don’t produce this phenomenon, it is the bacteria residing in these squids that produce this light. Together they can perform the largest symphony of dancing blue stars in the ocean.

The bacteria, Vibrio fischeri, is a symbiont that lives in the mantle of the Bobtail squids. The squids acquire this bacteria after they are hatched. These symbionts live in the deepest tract of the mantle and they produce the light source depending on the seawater environment, sensed through the squids’ pores. Furthermore, the Bobtail squids expel around 90-95% of these bacteria every dawn. At dusk, the bacteria increase in population and emit light again from the mantle. Since Euprymna scolopes is a nocturnal species, it hunts for prey at night time. With the bacteria, the squids are able to perform counterillumination. This effect allows them to camouflage themselves by looking like the sky above or deep abyss to divert their predators’ attention.

Here’s a video from the United Kingdom Society for Applied Microbiology uploaded by Siouxsie Wiles on YouTube. It explains how the Bobtail squids and the bacteria interact.

YouTube Preview Image


But here is the most astonishing hypothesis about the symbiotic relationship: the squids themselves can adjust the intensity of the light produced by their dependents.

Research tested this hypothesis and found two possible theories. Firstly, the squids may be controlling their oxygen intake to restrict the bacteria’s production of energy, thus resulting in dimmer or brighter illumination.  Secondly, the squids control light emission by using their ink sac as an iris to restrict light. Both processes cannot kill the bacteria but only limit its emission. Unfortunately, biologists couldn’t explain the mechanism behind light intensity control since they could not visually see inside the mantle.

Aliivibrio fischeri (toxita.cz)

A photo of the bacteria, Vibrio fischeri, which provides the Bobtail squid bioluminescence, in a petri dish. Photo from toxita.cz.

Biologists are trying to find out how these bacteria communicate with its host. There still remain many unanswered questions. For example, how do the squids know how much V. fischeri to expel? What happens if we remove these symbiotic bacteria from their hosts? How do the squids know when to stop before killing the bacteria?

With further research, they hope to understand how bacterial cells communicate with human cells using Bobtail squids as their model. Scientists wish to find ways to distinguish harmful bacteria versus those that help regulate our body. By understanding how V.fischeri functions inside the squids, we could produce antibiotics that only pinpoint the harmful bacteria in our body and find ways to disrupt these bacteria from causing us sicknesses.

– Alison Fung





Contact Lenses. Bye-bye Eye Sight

Do you wear contact lenses? I don’t. I don’t know how to order them, how to put them on, or how to clean them. But even though I have little to no knowledge on contact lenses, I do know this: Don’t sleep with them on!

About half of my friends wear contact lenses and at some point, I hear them say “I slept with my contact lenses on last night”. Guaranteed.

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The application of a contact lens. Source: Flickr Commons user suanie

At this point, some of you are probably thinking:

“Why do we say this?”

“What’s the reason for taking out contact lenses before bed?”

“What are the proper steps to cleaning them?”

Well, I am here to help answer these questions.

In a recent article published by CBC, ophthalmologist Tim Hillson addresses the fact that contact lenses prevent oxygen flow to the cornea, causing nutrient-providing blood vessels in the eye to expand. This makes the eye prone to infection. Leaving the contact lenses on over night allows bacteria build up that can penetrate the cornea.

There are 3 types of infection to the cornea:

Acanthamoeba keratitis: A rare infection caused by amoeba, often found in swimming pools, tap water, and hot tubs. May result in blindness.

Bacterial keratitis: An infection that proceeds rapidly. Caused by common bacteria like staphylococcuss aureus.

Fungal keratitis: An infection caused by a fungal organism. Usually involves pain in the eye.

Recently, Lian Kao, 23 year-old Taiwanese student became blind due to prolonged application of contact lenses. When I say prolonged – I mean 6 months! Kao did not remove her disposable contact lenses for 6 months straight, and even went swimming with them on. The cause of her blindness is said to be from Acanthamoeba (as described above), where amoeba ate her cornea during the course of 6 months.

An illustration of Amoeba proteus, by Joseph Leidy, 1879 − The organism that caused Lian Kao’s blindness. Rare but dangerous when infected. Source: Wikipedia

An illustration of Amoeba proteus, by Joseph Leidy, 1879 − The organism that caused Lian Kao’s blindness. Rare but dangerous when infected. Source: Wikipedia

Specialists say that the blindness caused by acanthamoeba is an extreme case, but they want the public to “realize the importance of using contact lenses as prescribed”. Well, I guess it is fair to say that Lian Kao learned it the hard way.

So how preventable are these infections? Easy. Just follow these 8 steps regularly.

  1. Wash and rinse hands with a mild non-cosmetic soap before handling contact lenses.
  2. Dry hands with a clean towel.
  3. It is a good idea to keep fingernails short and apply hair spray before you put in your contacts.
  4. Put on makeup after the contact lenses are in your eyes, and remove them before you remove your makeup.
  5. Always use disinfecting solutions that your eye care professional has recommended. Be aware that some eye products or eye drops are not safe for contact lens users.
  6. Never use tap water directly on the contact lenses, or put them in your mouth.
  7. Clean each contact by rubbing it gently with your index finger in the palm of your other hand.
  8. Clean contact lens case after every use, with either sterile solution or hot tap water and let it air dry. These cases should be replaced every three months.

Here is a video showing the steps, created by FramesDirect.com:

YouTube Preview Image

Aside from these steps, I also recommend getting eye exams or check ups regularly. Although you are not guaranteed protection from those nasty infections, just remember, doing something is better than doing nothing.

And again, don’t forget to take them out before going to bed.

-Lilly Inoue