2015 is the Year of the PHAGE!!!

Yes, they have given an entire YEAR to celebrate phage and the discovery of phage 100 years ago! There are a number of articles that discuss the illustrated history of phage and how we may use phage to try to stop bacterial infections, as well as the beauty and diversity of different phages. For the last one make sure to scroll through all the images at the top of the article. Here is an example of the beautiful images created by the artist, Ben Darby:

Salmonella phage gifsy-23

Salmonella phage gifsy-23

From the Illustrated History of phage research:

If tailed phages on the planet Earth were laid end to end they would extend for 200 million light years?

It is also an illustration of where we may be going with phage technology as well!!


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The facts about sun damage and suncreen

Ok, some of you are off for spring break to a place that is sunny and warm (hopefully). But new research from Yale University published in the journal Science (Feb.20, 2015)  indicates that UV irradiation causes both direct damage (DNA dimer formation that causes mis-reading of a DNA strand) during UV exposure, but can also create reactive oxygen and nitrogen species (free radicals) that act on the melanin in our skin for at least 3 hours AFTER exposure to UV light. This damage happens with BOTH  sun exposure as well as tanning bed exposure- any UV exposure.

This data  indicates that melanin that protects us from the sun, may also cause cancer as well. This reinforces the notion that there is no such thing as a protective “base tan”. It is all DNA damage, plain and simple. And will continue to harm you long after you leave the sun.

So… on that note, I wanted to let you all know that sunscreens work! But sunscreens are water-resistant, NOT waterproof, or sweatproof.  Water resistant means that they will protect you for about 40 or 80 minutes in the water (depending on the type you purchased), but then have to be reapplied. Also, did you know that an SPF rating of 15 absorbs 93% of UV rays, and that 30% absorbs 97%? Any sunscreen rated higher than an SPF of 30 may be fudging their numbers, as it is almost impossible to stop more than 97% of UV rays. And with this in mind from the same article:

The rules also say only sunscreens with a sun protection factor higher than 15 can claim to reduce the risk of skin cancer, aging, and sunburn, and that those rated SPF 2 to 14 must be clearly labeled as not doing so.

So that means, if you use a sunscreen with an SPF of less than 15%, you are at risk for ALL of those: aging, cancer and sunburn.

So remember, have fun in the sun, but use a sunscreen of at least 15% and reapply often!!!


Happy spring break.


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Great TED Talk about the human Microbiome by Rob Knight

Rob Knight is a pioneer in studying the human microbiome, and his TED Talk “How Our Microbes Make Us Who We Are” was all about just how important the microbiome is, how antibiotics may be altering important aspects of how it is supposed to function, as well as how he is using his lab to study how the microbiome changes over the course of a newborn’s life. It was amazing. I especially thought the aspects of how the microbiome makes us fat or thin was especially intriguing. I may stop dieting, and go searching for “skinny” microbiota….

As a matter of fact, it is so amazing, I signed up to become part of his research, the American Gut Project! For $99, I am getting my microbiome sequenced (using 16S ribosomal sequencing techniques). I will send him a sample of my microbiota (yes…that sample), and a detailed description of the food I eat, and what I do.

I will post more on the results when they come in!

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Leonard Nimoy died of COPD

Leonard Nimoy stated that although he quit smoking 30 years ago, it had had a lasting impact on his lungs. It is reported that he died from the effects of Chronic Obstructive Pulmonary Disease (COPD ).  COPD is caused when toxins in the air you breath (especially from cigarette smoke) destroy the surface area of the lungs, reduces lung capacity. It is estimated that 80% -90% of COPD related deaths are due to smoking/toxins in the air from secondhand smoke. COPD is the third leading cause of death in the US.

From the NIH COPD website, people with COPD:

  • Have a shortness of breath while doing everyday activities.
  • Produce excess sputum.
  • Cough frequently, or constantly.
  • Wheeze.
  • Feel like they can’t breathe.
  • Are unable to take a deep breath. 

The best and easiest way to avoid COPD is to not start smoking. If you do smoke, stop. Also, your children will be impacted by your secondhand smoke if you smoke around them. Secondhand smoke takes away their health by your habit.

It is best to Live Long and Prosper.

Goodbye Mr. Spock.

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How bacteria are winning the antibiotic war.

Bacteria are winning the antibiotic war, because we are giving them all the information they need to win.  How does this happen? Bacteria have been learning how to resist the antibiotics we have been taking for viral infections. ANTIBIOTICS CANNOT, DO NOT WORK AGAINST VIRAL INFECTIONS. Don’t believe me?

See the CDC Get Smart campaign:

Antibiotics do not fight infections caused by viruses like colds, most sore throats and bronchitis, and some ear infections. Unneeded antibiotics may lead to future antibiotic-resistant infections. Symptom relief might be the best treatment option.

or warnings from the  NIH:

If a virus is making you sick, taking antibiotics may do more harm than good. Each time you take antibiotics, you increase the chances that bacteria in your body will be able to resist them. Later, you could get or spread an infection that those antibiotics cannot cure.

Or alerts from the Mayo Clinic:

Antibiotics: Misuse puts you and others at risk

What are viral infections? According to the CDC, bronchitis is most commonly caused by a number of viruses, and only RARELY, bacteria

Causes of Bronchitis

  • Several types of viruses, most often:
    • Respiratory syncytial (sin-SIH-shull) virus (RSV)
    • Adenovirus
    • Influenza
    • Parainfluenza
  • Bacteria, in rare cases
  • Pollutants (airborne chemicals or irritants)

So based on the above, if you have bronchitis, antibiotics won’t help, and may actually hurt you.

Why is this important? Because bacteria are learning how to subvert the action of antibiotics and are spreading the message to other bacteria. We are losing our wonder drugs because…we think we can self diagnose and that antibiotics are useful in all situations.

Again, the words superbugs SHOULD alarm you.

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How to create an army of “Superbugs”

In a very good article, USA TODAY describes how hospitals across the US are fighting a “Superbug” war. What is a superbug? It is a bacterium that has gained the ability to be resistant to almost all available antibiotics. The article discusses CRE bacteria. In class I have discussed the NDM-1 plasmid which encodes an enzyme called carbapenemase, which cleaves carbapenam antibiotics (which up until now had the been the antibiotic of last resort for extensively resistant bacteria). Both  CRE and NDM-1 are not examples of specific bacteria, but of genes that can transfer resistance to a wide array of bacteria.  Any bacterium containing the genetic information would be resistant. Examples are that both  E. coli and Klebsiella pneumoniae are identified as CRE bacteria.

How does this happen? The animation in the USA Today story is perfect. We take an antibiotic that a SINGLE bacteria may be resistant to. Then, that one bacterium can do one of two things. They can simply grow to fill in the spaces left by the sensitive bacteria, or they can use horizontal gene transfer to transfer antibiotic resistance to other bacteria that hadn’t been antibiotic resistant. Horizontal gene transfer is the ability of bacteria to share genetic information with other bacteria in a population. (Vertical gene transfer is what happens normally when a bacterium divides and replicates it genetic information for its daughter cells).  The animation details horizontal gene transfer with both transposons transferring resistance as well as conjugative plasmids via conjugation.

In class, we discuss that once a bacterium gains a conjugative plasmid, it WANTS to share the information with other bacteria. This can create an entire army of bacteria that are superbugs. Where is the best place for this to happen? The human gut is a great place for bacteria to get together and exchange information.

How quickly can this spread? According to the article:

the first known case, at a North Carolina hospital, was reported in 2001, CREs have spread to at least 41 other states

The NDM-1 was first identified in Swedish patient who had visited India for surgery in 2008 and bacteria containing this plasmid has been found in: 

India, Pakistan, the United Kingdom, the United States,Canada,Japan and Brazil.

Currently, CRE and NDM-1 bacteria are found primarily in hospital settings. But the concerns are that, similarly to MRSA, these organisms will become more common outside the hospital among the general population, creating a serious healthcare problem that won’t…can’t…be treated with any currently antibiotic therapy.

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Understanding the influenza virus

There is a great  article in the online magazine Ars Technia  that details influenza viral replication and structure. It is essentially a re-print from a post from the epidemic of 2009 (there are a few details at the beginning regarding this year’s virus). However, what is there, is very good. It details how the virus replicates, what the H and N stand for in the viral names (hemagglutinin and neruaminidase) as well as how the virus infects.

If anyone in your family wants to know and understand influenza a little better this is a great article. One of the reasons I especially liked this article is because it details the fact that this is an RNA virus. More specifically, this virus needs not one, but requires THREE RNA dependent RNA polymerases (RDRPs) in order to make infectious virions:

Finally, the influenza virus’ genome exists as RNA, rather than DNA, and the (host) cell’s enzymes are not prepared to duplicate that or transcribe it into the messenger RNAs that get made into proteins. So, the flu virus brings its own, with three genes encoding RNA-dependent polymerases.

The article states that the best strategy for preventing the flu is a vaccine (killed or live attenuated), but that isn’t 100% effective (actually only 67% effective this year). If you do get the flu, this is a the best advise on what to do as holistic therapy in a  site  from the U.S. government:

You can treat flu symptoms without medication by:

  • Getting plenty of rest
  • Drinking clear fluids like water, broth, sports drinks, or electrolyte beverages to prevent becoming dehydrated
  • Placing a cool, damp washcloth on your forehead, arms, and legs to reduce discomfort associated with a fever
  • Putting a humidifier in your room to make breathing easier
  • Gargling salt water (1:1 ratio warm water to salt) to soothe a sore throat
  • Covering up with a warm blanket to calm chills

Little by little we are beginning to understand that Granny was WAY ahead of us in common sense treatments that actually work.

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OK, so I am not the only one who is slightly obsessive

Many thanks to Claus Ullstad  for sending me this. It is perfect. I would credit the author, but I don’t know who did this. Probably a microbiologist.

It's a virus

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Fecal transplants as standard operating procedure?

I tell my students that humans are essentially a donut.  Around the outside of the donut, we have our wall (skin/epidermis)  which separates the outside and inside. We humans know and expect to find bacteria there. But what people don’t think about  is that the donut hole, or the  tube down the middle of you that connects your mouth to your anus, is essentially outside, meaning it is full of stuff that simply passes through your body as well as a huge number of bacteria. The overall ratio of  bacteria cells  to human cells is about 10 to 1.

These bacteria that are found on our surfaces and in our tube have historically been called  commensal organisms: they benefited from us but did not help their human hosts. But not even Wikipedia calls them that anymore. This is because we now know that these microbes that colonize our skin and donut tube may be essential for human health. We now call them our  “human microbiome“. We are just beginning to understand that an intact microbiome can be as important as your immune system in keeping you healthy.  You can think of our microbiome as the organisms that we are just beginning to understant protect us  in a myriad of ways. One is simple one is to keep bad bacteria from getting established and running amok.

We now are aware that in fighting some deadly bacterial infections, we cause calamities in our microbiome. The antibiotics that are targeting pathogenic bacteria will also act on our essential gut bacteria.  When our microbiome is decimated this opens space for deadly invaders (such as Clostridium difficilealso known as C. diff) to gain a foothold. The problem with C. diff specifically is also that it is also very resistant to antibiotics.

Historically we have treated life threatening C. diff infections with higher and more dangerous levels of antibiotics.  A wonderful new article in the New York Times details the trials and tribulations of a C. diff infection as well as a new and exciting cure for this deadly infection.

Fecal transplants. Wait a minute. This is nothing any different than using a healthy microbiome as therapy/treatment.  Yes, this therapy sounds disgusting, but we now understand that  these bacteria, our microbiome, are fundamentally a PART OF US, an essential component to human health. Transplanting a microbiome is no different than any other form of transplantation where you take healthy tissue from one individual and give it to another. Physicians should stop using fecal and start using a microbiome transplant.

Research detailed in the New England Journal of Medicine describe the amazing results using fecal microbiome transplants. From the NYT article:

(fecal) transplants cured 15 of 16 people who had recurring infections with Clostridium difficile bacteria, whereas antibiotics cured only 3 of 13 and 4 of 13 patients in two comparison groups.

Amazing. 15 of 16. In another part of the NYT article they describe the symptoms of one patient in the study:

Melissa Cabral, 34, of Dighton, Mass., was healthy until she contracted C. difficile in July after taking an antibiotic for dental work. She had profuse diarrhea, uncontrollable vomiting and high fevers that landed her in the hospital. She suffered repeated bouts, lost 12 pounds and missed months of work. Her young children would find her lying on the bathroom floor.

They treated her without success with antibiotics. Within ONE DAY of a fecal microbiome transplant she was cured. ONE DAY.

The article from the New York Times is wonderful. It describes C. difficile, exactly what a fecal microbiome transplant consists of, as well as lots of fabulous reporting.

We are now essentially entering a new golden age of microbiology. This will show not just how bacteria can cause disease, but how bacteria can make us healthy.  Stay tuned.  This is going to be a wonderful ride.

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How long should you have a cough following bronchitis?

How long should you have a cough following bronchitis?  There was a great new article (I encourage you to read the actual article: link)  in USA Today detailing that a large majority of individuals don’t know the answer to this question. These individuals get  colds and coughs that last longer than they THINK they should.

The title of the article is perfect: Coughing for Two Weeks? You still don’t need an antibiotic.

The article is actually detailing research published in the Annals of Family Medicine. From that research , most people think they should be over a cough in 7-8 days. However, a cough caused by acute cough illness (ACI) commonly diagnosed as acute bronchitis, normally lasts upwards of 18 days.

This research then details that if the cough lasts longer than what is expected, we self-diagnose with a more severe disease such as pneumonia.

This is “because it isn’t normal for a cough to last that long”. This last sentence  is a direct quote from my sister with this exact problem. She had a cold. Her cough lasted longer than what she thought it should. She then made an appointment with a doctor, who told her she had a cold,  did NOT have pneumonia or any other serious problem.

He then prescribed her an antibiotic to take if she wanted to, or if she felt it was necessary. She called me because she knows I am a fanatic about improper use of antibiotics. What did I tell her to do? I asked her how bad her cough was (Not bad, but it had been going on since New Years). I asked her what her doctor said (no pneumonia, probably a cold). Then I told her to hang on to the prescription, but to get rest, drink a lot of  fluids and eat chicken soup.  I guaranteed her that she would feel better in three days without antibiotics.

Did she get better? Absolutely. Did she need antibiotics? Absolutely not. What was the best prescription for her? It really comes down to that so many of the things your Granny told you to do (as well as the Mayo Clinic) were right. Get lots of fluids, plenty of rest (this may actually mean taking a couple of days off work!! Yes, they will survive without you for a few days) and eat chicken soup.

More on this as the cold and flu season progresses.


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