Lab Report

Lab report data

Fall 2020

This assignment may be done in groups no larger than 3.  The score on this can replace your lowest test grade. 

These data were obtained because we were searching for antibiotic-producing soil bacteria.  We need new antibiotics because of the prevalence of resistant bacteria – we are a part of the Small World Initiative.  We took soil and did serial dilutions; we did Gram stains on four isolates, we identified an organism through a spread patch (since we skipped that lab the methods can just say “The antibiotic-producing isolate was identified through the spread patch method.”.  Then we used all our biochemical tests as well as DNA isolation, sequencing, and Geneious to identify the organism.  Sometimes the biochemical data conflicts with what the sequence identified which can be covered in the discussion.  The outline for the lab report is at the end of this document.

<Figure 1> Soil Plate: soil sample diluted to factor 10^(-5).

<Figure 2> Gram Staining Result of four different soil isolates:.

<Figure 3> Biochemical Tests (agar): Biochemical testing of YM1 was conducted on different kinds of agar plates, and only blood plate showed positive result after all of the testing.

<Figure 4> Biochemical Tests (tubes): From the left, these are testing results of Nitrate, MR, VP, Lactose, Glucose, Sucrose, Urea, Citrate, and TSI. Glucose carbohydrate test, Methyl Red Test, Nitrate reduction test, Citrate Test, and TSI showed positive results.

<Figure 5> Isolate identification using phylogenic tree: the tree created with help of Geneious software identified YM’s closest phylogenic resemblance to Leminorella Grimontii.

<Table 1> Biochemical test data table: this table shows all of biochemical testing methods utilized along with its result description and their significance.

<Table 2> Kirby Bauer Disk Zone of Inhibition Diameter Chart: On the original table of lab notebook, it showed all six ESCAPE pathogens’ result with their interaction to six different antibiotics. This table was abbreviated to contain result of E. aerogenes, which revealed zone of clearance when interacted with the YM1 soil isolate.

SWI Final Lab Paper Content – per group – no more than 4

The purpose of this assignment is to analyze the meaning of the data collected from the isolate.  You should imagine that the reader is an intro bio student at GGC.  This means you should explain jargon and walk your audience through the argument.  The structure and organization of this assignment is a standard scientific journal.

1. Introduction:

1. 1. Motivations

1. Why do we need new antibiotics? What are ESKAPE pathogens (we tested our soil isolates against a close and safe relative). How does antibiotic resistance happen (from molecular mechanisms inside cells to HGT)?
2. This isolate is or is not novel (newly discovered).

1. Materials and methods
   1. See lab lectures/handouts (Soil serial dilution through the tree).  Be very brief!
2. Results:
   1. Simply describe what you see – save interpretation until discussion.
3. Discussion
   1. What species is your isolate?  (Use sequence and/or biochem interpretation)

1. Why is it/isn’t it novel? Does it have antibiotic producing relative?

1. 1. Speculate on molecular basis of how it inhibited the ESKAPE relative. (use mechanism of relatives and the Kirby Bauer results, this applies the antibiotic lab).
   2. Summary

1. What was done, why we did it and if this isolate novel or not as well as why you think so.

A few special notes

1. Don’t interpret (say the meaning) of anything in Results section – just state the facts, describe what it means in discussion
2. I’d use a chart for biochem results – MR – red, Citrate – blue, etc
3. If confused about what’s a decent reference just ask
4. Third person past tense for methods and results
5. If you have a complete sentence that is cut and paste, it doesn’t matter if you cite it – it is plagiarism unless it has quotation marks around it. That’s a zero.