Human Oral Microbiome Database Lab Online- Madi Fishel by Madi Fishel

Corynebacterium diphtheriae

mafishel — 2021-03-15 18:11:49 UTC

Corynebacterium diphtheriae is a rod-shaped, Gram positive, non spore-forming, and nonmotile bacterium which is pathogenic and the main cause of diphtheria. This bacterium is also known as Klebs-Löffler bacillus because it was discovered in 1884 by Edwin Klebs and Friedrich Löffler.

Taxonomy: C. diptheriae

mafishel — 2021-03-15 18:22:48 UTC

Lifestyle Facts: C. diphtheriae

mafishel — 2021-03-15 18:26:06 UTC

Corynebacterium diphtheriae is responsible for causing the disease, diphtheria.
- Symptoms: The symptoms include sore throat, weakness, fever, and swollen glands. Also, a thick, gray coating can accumulate in the nasopharyngeal reason resulting in it being hard to breathe and swallow.
- Transmission: Diphtheria can be transmitted through water droplets in a cough or sneeze and enter the body through the nose, tonsils, and throat.
- Treatment: Patients with severe cases will be given a diphtheria antitoxin. Those who are patients or carriers of C. diphtheriae, will be given antibiotics such as Metronidazole, Erythromycin, and Procaine penicillin G. If left untreated, diphtheria can cause damage to the heart, kidneys and nerves. Suffocation and partial paralysis may be a result as well.
- Prevention: DTap is the vaccine that prevents this disease, which is mandatory for students and teachers.

Phylogenetic Tree

mafishel — 2021-03-16 13:15:45 UTC

Two closely related bacteria listed in this phylogenetic tree are Parascardovia denticolens and Bifidobacterium dentium. These two share the same Domain (Bacteria), Phylum (Actinobacteria), Class (Actinobacteria), Order (Bifidobacteriales), and Family (Bifidobacteriaceae). Not only that, but these two bacterium also are the causes of anaerobic diseases. Going down the line, the 'cousins' become more distantly related to each other. Specifically to Parascardovia denticolens and Bifidobacterium dentium, the bacteria most distantly related is Granulicatella elegans which has a completely different taxonomy compared to those listed above. It is also anaerobic unlike the pair above.

Kingella denitrificans

mafishel — 2021-03-16 20:56:48 UTC

K. denitrificans is a gram negative, anaerobic, coccobacilli which is colistin-resistant and isolated on selective medium for N. gonorrhoeae. K. denitrificans are opaque and grow on agar surfaces after incubating for 48 hours (as seen below).

First-line antibiotic susceptibility pattern of toxigenic Corynebacterium diphtheriae in Indonesia

mafishel — 2021-03-16 22:30:11 UTC

In Indonesia, there has been an outbreak of Diphtheria and studies have reported that resistance "to penicillin, erythromycin, and other antibiotics, single or multiple," have occurred. C. diphtheriae isolated were collected from patients. Of those 114 isolates, 108 were found to be viable and toxigenic. E-tests were performed on these isolates to find the susceptibility and minimum inhibitory concentrations (MIC) of five antibiotics known as penicillin, oxacillin, erythromycin, azithromycin, and clarithromycin. "The E-test result for penicillin was 68.52% susceptible, 31.48% intermediate, and 0% resistant (MIC range, < 0.016 to 2 μg/L) and for erythromycin (MIC range, < 0.016 to > 256 μg/L) was 85.2% susceptible, 12% intermediate, and 2.8% resistant The MIC range for oxacillin was 1 to 96 μg/L, while for both azithromycin and clarithromycin were < 0.016 to > 256 μg/L" [Quote]. The figure below shows the results of the tests ran which includes the Number of isolates (y-axis), MIC (x-axis), mitis (red), and gravis (blue)- which are the different biotypes of C. diphtheriae.

Lifestyle: K. denitrificans

mafishel — 2021-03-16 22:30:51 UTC

Causes diseases such as bacteremia, endocarditis, pediatric vaginitis, peritonitis in peritoneal dialysis patients, chorioamnionitis, and septicemic granulomatosis in AIDS patients. [Quote]

Reflection

mafishel — 2021-03-17 23:41:42 UTC

Throughout this process, I learned that examining the two sets of 16S rRNA can be a lengthy process; however, if done correctly it can lead to all of the right answers. Specifically in BLAST, I was able to identify my two unknowns just by entering the RNA genome as well as find the Taxonomy by the links provided in the database. I was also able to link these two pathogens in real life circumstances through research as well as through the phylogenetic tree- to see what these organisms are related to. The phylogenetic tree was easy to construct once I entered the tree information into the Clustal Omega database. The only setback of that was having to get rid of the numbers and entering an underscore between each species and genus. Though, in doing so, I believe I got accurate results in my phylogenetic tree and was able to learn more about these organisms through their lineage. The research, on the other hand, was a little more difficult for me. I had an easy time finding information and interesting articles about C. diphtheriae, but with K. denitrificans, I was having a hard time. I believe it was mostly because this organism was described as the rare genus in the Kingella species. Fortunately, I was able to find all the useful and interesting information needed to include in my Padlet. This assignment and the Ted Talk made me realize just how important studying the microbiome is. The microbiome is all around us, on us, and inside of us so knowing what these different microbes are responsible for is a must have to remain healthy. Also, the microbiome is constantly changing and developing, as noticed reading through these articles. For example, SARS in 2003 versus SARS now- there have been mutations causing different strains to develop. Knowing this information can help us find vaccines to prevent us from these infections and fight the pathogens.

Identification of a Large Family of Slam-Dependent Surface Lipoproteins in Gram-Negative Bacteria

mafishel — 2021-03-18 00:46:45 UTC

"The surfaces of many Gram-negative bacteria are decorated with soluble proteins anchored to the outer membrane via an acylated N-terminus; these proteins are referred to as surface lipoproteins" [Quote]. These scientists have identified a family of outer membrane proteins known as Surface lipoprotein assembly modulator (Slam). In this study, bioinformatic analysis was used to identify 832 Slam related sequences in 638 Gram-negative bacterial species, which includes human pathogens previously reported as not having SLP's. 353 out of the 832 Slam related genes were identified and 185 out of the 353 clusters Slam related genes contained lipoprotein-encoding genes- the list including three confirmed SLPs including Kingella denitrificans which is a HpuA homolog.