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Gut Microbiome and Backyard Chickens

Chickens in Backyard ImageI was talking to someone recently about backyard chickens. The topic came up because there was a newspaper article about an increased chance of exposure to Salmonella from handling chickens. It reminded me that early in my teaching career, a fairly large turtle was donated to me for my classroom. My plan to use this turtle to stimulate student interest came to a quick halt when one of my administrators told me that I couldn’t keep the animal in the classroom as it was a source of Salmonella. It also reminded me that at one time the Alberta Science curriculum had a significant unit on ‘Micro-organisms and Food’. Salmonellosis was a topic of much discussion along with staphylococcal food poisoning, giardiasis and shigellosis.

Salmonellosis results from exposure to Salmonella. It is one of the most common food related diseases, leading in some accounts to the most employee absences due to illness. The symptoms, which include diarrhea, fever, and abdominal cramps, are often described as ‘stomach flu’. It is interesting to note that norovirus causes similar symptoms and is also described as stomach flu. Neither norovirus nor Salmonella are actually related to flu, which is caused by the influenza virus.

One possible reason that Salmonella can lead to symptoms of food poisoning is that these bacteria produce gas and possibly toxins when they multiply in our digestive system. Although it is not a normal part of the gut microbiome, Salmonella is a common gut bacterium in reptiles and can be found frequently in birds as well. Salmonella was first discovered by William Budd in 1873 and first successfully cultivated as a pure culture in 1884. Mapping the Salmonella genome has been a long term project. In the early 1950s, genetic experiments were being conducted with Salmonella on conjugation and transduction before Watson and Crick had even developed their DNA model. Since the 1960s, the Salmonella Genetic Stock Centre has been maintained by Dr. K.E. Sanderson and housed at the University of Calgary.

According to the Centers for Disease Control and Prevention:

Salmonella are usually transmitted to humans by eating foods contaminated with animal feces.”


Salmonella may also be found in the feces of some pets, especially those with diarrhea, and people can become infected if they do not wash their hands after contact with pets or pet feces. Reptiles, such as turtles, lizards, and snakes, are particularly likely to harbor Salmonella. Many chicks and young birds carry Salmonella in their feces. People should always wash their hands immediately after handling a reptile or bird, even if the animal is healthy. Adults should also assure that children wash their hands after handling a reptile or bird, or after touching its environment.”


“Cross-contamination of foods should be avoided. Uncooked meats should be kept separate from produce, cooked foods, and ready-to-eat foods. Hands, cutting boards, counters, knives, and other utensils should be washed thoroughly after touching uncooked foods. Hands should be washed before handling food, and between handling different food items.”

In Alberta, there is an increased chance that you will be exposed to urban chickens. Edmonton and Red Deer already allow them, and Calgary politicians are being pressured to approve backyard chicken coops. Here are some of the things you need to know:

  • Urban chicken farmers have their greatest success when they handle and calm their chickens. This allows them to enter the coop without the chickens flying in frenzy up into the beams or wire which could injure the chickens. 
  • Children are at the greatest risk of exposure to Salmonella. The children may handle or even try to kiss the very docile urban chickens and then fail to wash their hands thoroughly. 
  • • Since Salmonella is a normal gut bacteria in chickens, even healthy organic chickens can have Salmonella. The germs can be found on the feathers, on cages, coops, feed and water dishes and hay. 
  • Salmonella can get into the soil in the area where the birds are kept. 
  • Salmonella germs can be found on the hands, shoes, and clothing of those who handle the birds or work or play where the chickens roam. These germs can be tracked into the house. No urban farmer should ever use the 5 second rule for food dropped on the floor. 
Here is a thought for urban chicken farmers: probiotics.

In ecology, we learn about Gause's law a.k.a. the competitive exclusion principle. Through experiments, Georgy Gause found that when two species of Paramecium are grown at the same time in the same environment, one species will outcompete the other. In simplest language, two species cannot occupy the same niche at the same time. Here is where the probiotics for chickens come into play. Feeding baby chicks with special probiotics can lead to the exclusion of Salmonella without having to resort to the use of antibiotics. While this will not remove the need for hand washing and other precautions, it is one more natural way to reduce the probability of contracting salmonellosis.

Studying the gut microbiome has changed since the advent of metagenomics. There is no longer a need to isolate the bacteria or grow pure cultures. There has been such a frenzy of new research that the Twitter community had fun earlier this year with the hashtag #GutMicrobiomeAndRandomThing. One of my favorites was ‘Gut Microbiome And Always Ending Up Standing In The Slowest Line At The Cash Register.’ Seriously though, I think we can look forward to a lot of new and exciting research in this field. Génome Québec recently announced a major international research project:

“Lawrence Goodridge of McGill University and Roger C. Levesque from Institute for Integrative Systems Biology of Université Laval are leading a team that is using whole genome sequencing to identify the specific Salmonella strains that cause human disease. With this knowledge, the team will develop natural biosolutions to control the presence of Salmonella in fruit and vegetables as they are growing in the field. The team will also develop new tests to rapidly and efficiently detect the presence of Salmonella on fresh produce before it is sold to consumers, as well as tools to allow public health officials to determine the source of Salmonella outbreaks when they occur, so that contaminated food can be quickly removed from grocery stores and restaurants. Their work will reduce the number of people infected with Salmonella each year, as well as the economic costs of the infection.”

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