Microbiology Assignment 2 PDF

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Nam: Rebecca Simmons

Assignment 2

This week’s assignment is pretty simple. Eat a species/variety of food that you don’t normally, or have never eaten before. The food should be substantively different than what you generally eat. For example, if you rarely eat carrots but commonly eat potato chips, carrot sticks count, but veggie straws don’t. Pay attention to how you feel after you eat it. If for some reason your diet is so restrictive that you cannot eat something different, you may pretend you ate something and answer the following questions hypothetically. Don’t eat anything that you know will make you ill. Part 1: (Complete for class 9/11) (15 points 2.5 each) 1. What did you eat that you don’t normally eat? I ate Dominos new 6 cheese pizza (only 1 slice).

2. Did you enjoy it? Yes I did, I have an allergy to lactose (2 different proteins I believe) so I rarely eat cheese or any other dairy.

3. The foods we consume are likely to affect our gut flora in at least three major ways. A) By feeding the microbes that are present in our digestive tract. Prebiotics are foods that are marketed as feeding one’s gut flora in a beneficial way, but foods can also feed our gut flora in detrimental ways. a. How is a lactose intolerant individual over-indulging in lactose an example of feeding the gut flora in a detrimental way? (You may have to look this one up.) With my understanding I would say that most gut flora eats things that we cannot digest. So, if an individual is lactose intolerant maybe they don’t produce the right enzymes that can break down lactose. So, then if the individual eats a lot of lactose they wont be able to digest it and the gut flora will be affected. “The symptoms of lactose intolerance include diarrhea, stomach pain, cramps, bloating and flatulence, all of which result from failure to break down lactose in the small intestine. As undigested lactose moves into the large intestine, water enters to reduce the lactose concentration, producing diarrhea. The lactose is eventually eaten by microorganisms in the large intestine, producing, as byproducts, various gases that cause bloating, cramping and flatulence.” https://www.cnn.com/2019/04/17/health/lactose-intolerance-microbiomepartner/index.html

b. Recall that the primary source of food for the gut flora are substances that the human body does not absorb / cannot digest such as fiber, hard to digest starches, etc. How would switching from a low fiber, low starch diet to a diet that contains a lot of beans and whole grains effect the amount of food the gut flora has available? Eating an excess amount of food that your gut flora has available will make the gut flora flourish, maybe reproducing more and might cause the individual to have an increased amount of overall flora. Or it could kill gut flora. B) By biochemically affecting the ability of microbes to grow in the digestive tract. Penicillin is a bacteriocidal antibiotic produced by a number of fungal species belonging to the genus Penicillium, and as it turns out the Penicillium genus is also used to produce a number of foods (blue cheese, certain fuet sausage, etc.) While cheese fungi don’t typically produce penicillin, fuet sausages have been found to sometimes contain penicillin. What effect might over-indulging in these sausages do to the gut flora? This will probably result in the same way as the previous 2 examples. However, I believe that penicillin could potentially kill some of the needed gut flora that we have. C) By containing microbes, a number of foods, often referred to as probiotics, can affect the gut flora through direct consumption of microbes (typically bacteria or yeasts). These microbes may linger in the digestive tract after consumption of the foods and/or the presence of microbial compounds in the foods themselves may biochemically affect the ability of microbes to grow in the digestive tract. There is some evidence that appropriate consumption of probiotics may be beneficial to human health, but why might over-indulging in a probiotic be detrimental? I could see probiotics harming an individual in a few ways. I think that maybe probiotics could take away from the “good” gut flora that already exist in your intestines, removing the layer of mucus maybe that lines them. 4. Comparing the food to those foods that you usually eat, is the food more or less likely to contain different poorly digestible nutrients that might feed your gut flora? (Is it full of complex carbs, does it have a lot of fiber, full of polyphenols, etc.) My example was of lactose so, yes, it will be poorly digested in my gut by the gut flora. 5. Are you aware of any anti-microbial, anti-bacterial, and or anti-fungal claims about the food that you ate. (examples: ginger, garlic, etc.) I hear a LOT of claims about dairy/lactose etc. I have heard that you can make yourself not lactose intolerant, I have heard that 75% of people actually are lactose intolerant, I have heard that I can eat lactose if its from goats/sheep but not from cows. I am not sure what to believe, all I know is that this class will help me form my understanding of lactose and gut flora (thankfully).

Also, I know that lactose simply just isn’t good for me because I usually feel quite tired, cramp a little bit and have non-normal bowel movements afterwards, so ill steer clear. 6. Was the food likely to have bacteria on it that you don’t normally eat? Keep in mind that most processed and/or cooked foods will likely have very few bacteria that survive preparation. Yes

Review (20 points 2 points each) 1) _Sex, E. Coli_____ Is the most common cause of UTI’s. 2) This organism uses __pili ( don’t know if im spelling it right)______ to bind to the urothelium. 3) This organism (and many like it) relies on ____DNA Gyrase___ to relieve tension during DNA replication caused by the forward progression of helicase. 4) This enzyme ___negatively______ (positively or negatively) supercoils DNA, undoing the ______positive_______ (positive or negative) supercoils that result from replication fork progression. 5) This kind of supercoiling is when additional twists are put into DNA. (True or false?) false 6) ____Ciprofloxacin_______ inhibits the enzyme that is the answer to question 3, and is used as an antibiotic. It is part of the ___________fluoroquinolones______ class of antibiotics. 7) This antibiotic is good at treating urinary tract infections because: a. It’s secreted by the kidneys in mostly the same form it was administered. b. It’s secreted by the kidneys in a more active form. c. It’s particularly good at withstanding the toxic environment of the bladder. d. It’s particularly good at withstanding the toxic environment produced by the bacterium. 8) Short answer: How does the antibiotic inhibit bacterial DNA replication? Also, what are catenanes, and how does the antibiotic relate to their formation and/or resolution? Puts bacteria in stasis by inhibiting DNA gyrase. A catenane is two interlocked loops of DNA. It impossible for the cell to divide until DNA gyrase comes in, to un-lock them so we have 2 separate genomes.

9) Gram ________ (negative or positive) bacteria have a second membrane as part of their cell wall.

10) Short answer: most bacteria have how many origins of replication, how is this different from humans, and why does it make sense that humans have a different number from bacteria? MOST BACTERIAL CELLS HAVE A SINGLE ORIGIN. SIZE OF CHROMOSOMES Bacteria have about 350 origins, humans have about 40-80 thousand origins. I think this has a lot to do that bacteria are prokaryotes and humans are eukaryotes, so replication is different.

Part 2: (Be prepared to discuss 9/14) (55 pts) Monday we’re flipping the classroom! At our digital meeting, we’ll be discussing Campylobacter jejuni infection. In order to prepare, please use the paper “Global epidemiology of Campylobacter infection” (PMID: 26062576) to answer the following questions: 1) What is C. jejuni, and what is the infection that Campylobacter mostly causes in humans? Gram - can also lead to autoimmune disorders 2) C. jejuni is an example of a zoonotic disease, what animal do humans most commonly get C. jejuni from? Cattle chickens, meat, cats, dogs, 3) In the developing world, why is Campylobacter caused diarrhea most common in children? Exposure in early life might help you gain immunity. 4) In the developed world, why is Campylobacter infection less age specific? I think that travel can have to do with when people get it, so if you don’t travel on planes when your young then you travel when your older on planes you can catch it. Also, in the developed world we have much cleaner living spaces, and public spaces, and can easily sanitize etc. 5) What is one reason that drinking unpasteurized milk is a bad idea? Source of other strains of bacteria. 6) Pick one of the “other gastrointestinal diseases.” Read the section for that disease. What is that disease, and what did you learn? I read briefly about esophageal diseases. One that stuck out to me was GERD (Gastroesophageal reflux disease since my friend has acid reflux. I learned that you can get BE (Barnetts esophagus) from it and found it interesting that bacteria play a key role in this disease. “ Furthermore, the authors showed a strong correlation between C. concisus colonization and production of interleukin-18 (IL-18) (119), a cytokine that stimulates both innate and adaptive immune responses and has been widely associated with carcinogenesis” 7) Repeat 6 for the “Extragastrointestinal Manifestations” part of the review. I read about cardiovascular complications because I myself have one! I found it interesting that evidence suggests that certain bacteria have a strong correlation with certain heart

conditions/complications. Myo(peri)carditis is associated with bacterial entities and is a condition that shows up in people who are immunocompetent. ” Salmonella and Shigella are the main gastrointestinal pathogens linked to myo(peri)carditis, but the increasing incidence of campylobacteriosis worldwide over the last 10 years has drawn attention to Campylobacter-associated myo(peri)carditis.” 8) What are the two major classes of antibiotics that are discussed as being used to treat Campylobacter infection. What are macrolide antibiotics, and what is an example of one? Based on their mechanism why would you expect them to be bacteriostatic? Ciprofloxacin, a fluoroquinolone are most often used to treat Campylobacter. Macrolides: “Macrolides bind to the 23S rRNA nucleotides 2,058 and 2,059 in the 50S ribosomal subunit, which results in blockage of the translocation step of protein synthesis, thereby preventing release of tRNA after peptide bond formation and resulting in the termination of peptide chain elongation.“ Azithromycin is an example of one. I would expect them to be bacteriostatic because they don’t kill the bacteria, rather they, bind to them and stop their ability to reproduce. 9) Pick a subsection of: “Controlling the spread of campylobacteriosis” and summarize it. Reducing Campylobacter transmission in chickens: Once Campylobacter is introduced to a flock of chickens it spreads insanely rapidly, as it colonizes in the intestinal track. There are virtually no side effects to be shown except maybe diarrhea and inflammation. Luckily, passing it on to offspring pre-fertilization is rare but possible. Farmers should have strict hygiene routines in order to not come into contact, as human and vehicular traffic is the main route for this disease. 10) What is something interesting you saw in the article? I found most of the article interesting. I think its interesting that they are using bacteriophages for studying ways to get rid of the disease. Specifically because last year in bio 105 we found our own bacteriophages. To be completed following class: 11) What’s something else you learned during your discussion today? That there is never ending information about bacteria and disease and I have a lot of learning to do. Specifically, I liked learning about gut flora and how many little things are living (and helping us live) in our guts. 12) Why is Campylobacter infection a lot less common in the United States than in the developing world?

Maybe because of higher risk of contaminated food or water in developing countries. Also, in developing countries they lack national surveillance programs to track and help with the burden of disease. 13) What steps can you take to protect yourself against Campylobacter? Wash/sanitize your hands and food. Avoid unpasteurized milk, cooking your food fully, and be careful when dealing with animals. 14) How are macrolide antibiotics similar to tetracycline antibiotics? Tetracycline prevents the growth and spread of bacteria. Macrolides also inhibit the growth of bacteria....