New evidence that the microbiome is important in protecting against allergies and asthma!!

A new study published in the journal Science Translational Medicine  and discussed in the journal Science this week illustrates the importance of a normal microbiome and what changes in your microbiota may mean for long term health.

To look find associations between microbiota and disease, scientist have been looking at the entire microbiome. They do this using something called high-throughput genetic sequencing of the 16S ribosomal DNA sequence. The researchers who published this study were from the University of British Columbia in Vancouver, and investigated the microbiome of 319 babies at both the 3 month and at the 1 year mark. They then tracked the health of these babies over 5 years (where they looked at overall health at the 1 year/3 year/5 year time points).

Researchers found a significant difference in 4 key populations of bacteria. Children who were low or missing these four types of bacteria had a much higher chance to go on to develop asthma as they aged. The key missing bacteria were from the genera Lachnospira, Veillonella, Faecalibacterium, and Rothia. 

First of all let me stress: These are NOT bacteria that come from eating yogurt or taking probiotics. These are specific bacteria found in the normal guts of newborn infants and were only found using this new method of sequencing ALL the bacteria found in the gut. It is important to note that only these new techniques allow us to see and compare all the bacteria in the gut  (it is be very hard to culture or identify even a fraction of the normal microbiome using the old standard techniques for bacterial identification).

But to prove it was the loss of these missing organisms that were CAUSING the problem, mice grown in a germ free environment were given microbiota from babies in the study lacking these four kinds of bacteria. The mice given this type of flora developed inflamed lungs similar to what is seen in asthma.

When they reconstituted the mice with microbiota containing high levels of the four key genera of bacteria, mice were no longer at risk for developing asthma!!!

The scientists in the study were also looking for commonalities in the babies that were missing the important microflora. Were they delivered by C section? Were they given more antibiotics? Were they breast-fed or given formula? Did they live in the city or on a farm. This study indicated that the only factor that seemed to predict the loss of these important four types of bacteria was early exposure to antibiotics.

They are going to continue look to determine if the identification of missing specific organisms in the microbiota of newborns could be an early detection system for allergy and asthma in the future. Also, they are looking to determine if reconstitution of the missing bacteria could be protective!

Stay tuned for more!!!


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Consumer Reports details information on ground beef contamination with bacterial pathogens

In my previous blog post, I was discussing how Consumer Reports had conducted an investigation into contamination of retail chicken with known bacterial pathogens. We then discussed in class ground beef, and the likelihood that it will always be contaminated with bacteria. Consumer Reports came through for me again, and in their report: How safe is your ground beef?, they essentially proved me correct. Most ground beef, simply by the way it is processed, would generally be exposed to colicoliform bacteria (bacteria found in poop). What they found was all samples tested contained these bacteria.

And before we go any further,  let me stress, that thoroughly cooked hamburger is completely safe. Once your food is cooked (this means inner temp of your burger) is at 160 degrees F, the bacteria that are there are dead. Dead bacteria cannot hurt you. However, if your burger is pink inside, the bacteria that are there are still viable.

What kinds of bacteria did they find? They tested 300 samples of ground beef from various sources- big box stores, whole food stores (conventionally raised cattle, and those from sustainably raised cattle) . They tested for the five main types of bacteria that are indicated in disease from contaminated food: Various strains of E. coli (including O157),  Clostridium perfringens, Staphylococcus aureus, Salmonella, and Enterococcus.

20% contaminated with C. perfringens
10% with S. aureus- strains that included food superantigens

But worse yet, 18% ground beef from conventionally raised cattle were contaminated with superbugs (bacteria resistant to three or more antibiotics). Ground beef from sustainably raised  cattle had 9% contamination from superbugs.

More about this tomorrow….

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Is there still viable (living) bacteria on a frozen chicken?

Can bacteria survive the freezer?

Bacteria will freeze along with the food they are on when they are stuck into a freezer. The pathogenic bacteria on foods that cause human disease  are primarily mesophiles or organisms that grow best at around 37 degrees Celsius.  In a freezer at -20 degrees Celsius, their bacterial enzymes cannot function because the water inside the cell has frozen, so they cannot grow. It has been reported that if you put a raw chicken into your freezer (considered a slow freeze), you may reduce the number of bacteria by approximately 90%. This is primarily due to the formation of ice crystals in the bacterial cytoplasm which then ruptures the bacterial cell wall and kills the cell, reducing the number of viable bacteria.  In many food processing plants, food is flash frozen in a way that fewer ice crystals form in the food so more bacteria survive as well (up to 70 percent survive as opposed to 10 percent).

So the problem is the exponential growth capacity of bacteria. If the food is thawed improperly, (at room temperature) surviving bacteria on the surface can quickly reproduce to pre-freeze levels (USDA source).  So when is this a problem?

Let’s use chicken as an example food. In a Consumer Reports article in 2013, chicken from retail stores around the country were tested and Salmonella was found on 10.8 percent and Campylobacter on 43 percent of all samples tested. Just this spring in the UK, they tested over 4000 samples and found that 73 percent of all chicken tested were positive for Campylobacter. Worse yet, of those,  19 percent were deemed heavily contaminated. So even ten percent of these organisms on the thawed bird would be a serious contamination issue.

The other way that we know that bacteria survive freezing is just to check the news and the various outbreaks of illnesses linked to frozen foods. There was an outbreak in March, 2013 of E. coli O121 that sickened 24 people in 18 states  linked to frozen chicken quesadillas. The most recent outbreak is actually ongoing, where they have linked raw, frozen, Stuffed Chicken Entrees by Barber Foods to a Salmonella outbreak that has sickened 9 people in four states. Not only have these people become seriously ill, but the CDC identified that the strain of Salmonella responsible for the outbreak is a multi-drug resistant strain impervious to both tetracycline and ampicillin.

Best case practices in the case of contaminated foods? For pre-cooked food such as the quesadillas, reheat according to directions on box. Bacteria are killed by reaching temperatures of 165F, even muti-drug resistant bacteria.

For raw food, such as chicken, make sure to use aseptic technique when handling the food. Don’t touch surfaces of the kitchen with hands that have come into contact with the bird. Watch where the juice from the thawed chicken lands (it will be full of viable bacteria). Don’t wash your chicken in the sink, it aerosolizes the bacteria, and they may land on other surfaces that you are not aware of. NPR had a nice overview of what to do if you want to brine your chicken or marinade,-just remember that this fluid has bacteria in it and be careful when you are pulling the chicken out as to where the water droplets go. Thaw food in your refrigerator, in cold water, or in brine.

I always have a dish of hot soap water ready and wash my hands a lot when handling raw chicken. I turn on my faucet to wash my hands with my arm. Washing hands with soap is sufficient to prevent contamination. I also have my sink empty and all counter surfaces clear so that if anything DOES land there, it is a simple soap and water clean up.



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Canadian outbreak of O157:H7 due to contaminated leafy greens

A new outbreak of the strain of E. coli O157:H7 has just occurred in Canada. There have been just 12 cases, but all of the bacteria in those cases have exhibited the same genetic fingerprint, indicating an a common source epidemic (one that arises from a contaminated food source). Epidemiologists investigating the outbreak have not identified one food, but leafy greens.

The Public Health Agency of Canada is warning people to wash all food, keep refrigerated properly and use aseptic technique! From the article:

The following tips will help you reduce your risk of infection with E. coli or other food-borne illnesses:

  • Wash fresh fruits and vegetables before eating them, clean counters and cutting boards and wash your hands regularly.
  • Bacteria can grow in the danger zone between 4 °C and 60 °C (40 °F to 140 °F). Keep cold foods cold at or below 4 °C (40 °F) and keep hot foods hot at or above 60 °C (140 °F).
  • Keep refrigerators clean and at a temperature below 4 °C (40 °F). Install a thermometer in your fridge to be sure.
  • Place raw meat, poultry and seafood in containers on the bottom shelf of the refrigerator. Use containers that are large enough to prevent raw juices from dripping onto other food or touching other food.
  • Keep raw food away from other food while shopping, storing, preparing and serving foods.
  • Read labels and follow cooking and storage instructions for all food. When buying food, make sure to check the “best before” date, and if the product has expired, let the store know.
  • Use warm soapy water to clean knives, cutting boards, utensils, your hands and any surfaces that have come in contact with food, especially meat and fish.
  • Refrigerate or freeze perishable food within two hours of cooking.
  • Freeze or consume leftovers within four days of cooking. Always reheat leftovers until steaming hot before eating.
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Outbreak of Scarlet Fever in the UK

There is an outbreak of scarlet fever occurring in the UK. What makes this different from a regular Strep sore throat (caused by Streptococcus pyogenes) is that the strains of Strep causing these outbreaks encode a gene that allows them to produce a superantigen-exotoxin. This causes the non-specific activation of T helper cells, and creates the characteristic signs and symptoms of a sandpaper rash, and strawberry tongue.

But it is interesting how the signs and symptoms develop. First comes the typical Strep sore throat signs, a sore throat and a fever. Then, 12-48 hours after the first signs develop, the effect of the exotoxin becomes apparent, causing the effects of activation of non-specific T helper cells (the superantigen exotoxin binds outside of the antigen-binding site on the MHC class II molecule, allowing TCRs on T helper cells to non-specifically interact with these MHC molecules, and become activated.

The other thing to note, is that the effects of this toxin are relatively mild, and the threat to the child is the same as that of a regular Strep sore throat. In a patient under the age of 18, it should be treated immediately with antibiotics to prevent the Strep sore throat sequelae: Rheumatic fever or kidney failure, that occurs as a consequence of mounting an antibody response to specific strains of Streptococcus pyogenes.


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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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