Experts May Have Finally Found The Cause Of Crohn's Disease
Great news for those with the notoriously hard to treat condition.

People with Crohn’s disease know the uncomfortable symptoms of the chronic condition all too well: diarrhea, abdominal pain, weight loss and fatigue, among others. But what doctors have not been able to tell the approximately 565,000 people in the U.S. with Crohn’s is why they’ve developed the inflammatory bowel condition in the first place.

Most experts suspect the condition is the result of the body’s immune system attacking healthy cells, mistakenly triggered by bacteria in the digestive tract. Now, a new study has identified a specific fungus and two bacteria they think play a key role in what leads some people to develop the disease.

“Among hundreds of bacterial and fungal species inhabiting the intestines, it is telling that the three we identified were so highly correlated in Crohn’s patients,” the study’s senior author Mahmoud A. Ghannoum, professor and director of the Center for Medical Mycology at Case Western Reserve and University Hospitals Cleveland Medical Center, said in a press release.

Research has previously identified that E. coli bacteria contribute to Crohn’s symptoms, but this is the first study to show the bacteria Serratia marcescens and the fungus Candida tropicalis are also involved.

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Serratia flowers

Serratia marcescens can form brilliant red colonies on LB agar due to the synthesis of the secondary metabolite prodigiosin. In the Microbiology teachinglab, we had students create pigment mutants of S. marcescens and these lovely shades of pink and white were collected for analysis.

This photo was taken from our Submitted by: Phages_for_all_ages Thanks to the author(s): UIUC

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We are what we eat: Contributions to the microbial zoo within our guts

We celebrated International Pathology Day 2015 a couple of days back (18 Nov 2015). One of the activities at our booth was the chance to streak an agar plate with some familiar food and drink items-namely chicken rice chili sauce, sugar cane juice and carrot juice. There were 199 participants and they will get to see the results of their efforts on our Facebook page today (20 Nov 2015) around  1300 local time (0500 GMT).

The purpose of this exercise was two-fold. First it gave participants the opportunity to try their hand at one of the most fundamental techniques in microbiology. Second (after they see the results), it hopefully will provoke them to think about how we sometimes unwittingly acquire the bacteria that inhabit our innards. 

If you think about it, when we are formed in the womb, our guts are sterile. We usually acquire our first dose of bacteria while travelling down our mother’s birth canal. We continue to add to this initial stock of bacteria for the remainder of our lives. So every time you go to the toilet for a poop, consider that the smelly deposit you leave behind represents an incomplete record of

1. times you played in the playground as a kid and failed to wash your hands afterwards before snacking.
2. items you ate or drank that weren’t thoroughly cooked
3. etc…you get the idea

So what were the bacteria that grew out of our samples?

The chicken rice chili sauce had the lowest colony counts and least variety, which is not surprising since some of the ingredients (chili, ginger, garlic and vinegar) inhibit bacterial growth. Bacilis subtilis is a Gram positive rod commonly found in the environment that is non-pathogenic for humans.

In carrot juice, Enterobacter ludwigii has been associated with urinary tract, respiratory tract, and blood infections. Rahnella aquatilis as its name suggests is an environmental Gram negative rod associated with water and is of no clinical significance. Pantoea spp. are plant pathogens that occasionally cause human infections.

In sugar cane juice, both Klebsiella pneumoniae and Serratia marcescens are associated with human infections.

What are we to make of this? Well clearly most of us (myself included) drink fresh fruit juice regularly with no ill effects. These bacteria probably do not directly cause disease as a result of ingestion and therefore do not pose a problem to healthy people. However if you are a patient with a problem with your immune system you may want to avoid that sugar cane juice you left overnight in the fridge.


Some pictures taken in micro today. The two slides on the microscope are of Bacillus. The red rod-shaped bacteria are the actual bacilli, and those green dots you see are called endospores.

Endospores are formed when essential nutrients or other environmental standards are not being met. They’re extremely heat and chemical resistant. They are formed within the cell by the bacteria replicating it’s DNA. Those spores you see are very tough protective structures that house that replicated DNA after the mother cell ceases to exist.

Also, I made a chicken out of Serratia.



1. Vogesella indigofera, obtained from a pond brimming with highly toxic waste.

2. Pseudomonas aeruginosa, an opportunistic pathogen that can also be used in the bioremediation of oil spills.

3. A battle between Serratia marcescens (red) and the common soil bacterium, Bacillus mycoides (white). The Serratia seems to produce an antibiotic to protect itself from the invading Bacillus strain.