20.109(S14):Microbiome summary

Overview

The primary assignment for Module 1 will consist of two elements: an abstract that succinctly describes your bird microbiota investigation, and a thorough summary of your data in figures and supporting text – including context for understanding the work’s broader implications.

The target audience for this report is a scientifically literate reader who is unfamiliar with your specific field. Thus, you can assume rapid comprehension – but not a priori knowledge – of technical information, and consequently should strive to present your work in a logical, step-by-step fashion.

Logistics

You will complete this assignment in pairs. Be sure to review the 20.109 statement on collaboration and integrity as you proceed.

Method of Submission

Please submit your completed summary on Stellar, with filename TeamColor _LabSection_Mod1.pdf (for example, Rainbow_TR_Mod1.pdf).

Be sure to review the class late policy (link) as well as the further clarification below.

Submit First Draft: March 11th/12th

Revised to Friday, March 12th at 1 PM for both sections.

The first draft of your research article is due by 11 am on March 11th (Tuesday) or March 12th (Wednesday), according to which day you have lab.

Professor Runstadler will comment on your submissions and assign them a draft grade. Additionally, a writing instructor will give feedback about abstract structure and comprehensibility.

Submit Revision: April 3rd/4th

Revised to Friday, April 4th at 1 PM for both sections.

Your commented first draft will be returned on March 20th (Thursday) or 21st (Friday). (Revised to Friday, March 21st for both sections.) You will then have the opportunity to revise your report for up to a one and one-third letter grade improvement. In other words, a C can be revised up to a B+, a C+ to an A-, a B- to an A, etc. )

The final draft is due by 11 am on April 3rd (Thursday) or April 4th (Friday), according to which day you have lab.

Please briefly summarize any substantial revisions to your text in the “notes” section of the slide. (For example, “this slide was substantially revised to clarify the figure and deepen the analysis.) In addition, you may directly highlight revisions to your text – for example, by using a different colored font – when this approach seems useful.

Late Policy Clarification

Penalties for a late draft are direct. A late draft that is not revised will have the penalized grade recorded. For example, a B paper that is one day late and not revised will be recorded as a B-. If submitted on time, the B paper could go up to an A+, while the penalized B- paper can go up "only" to an A.

Penalties for a late revision affect the maximum possible grade. A revision that is one day late can only go up one full letter grade, one that is two days late can only increase by two-thirds of a letter grade, etc. For example, a B paper that is not late can earn up to an A+, that is one day late can earn an A, that is two days late can earn an A-, that is three days late can earn a B+, and that is four days late cannot improve on the B.

Guidelines on Formatting and Length

We recommend that you prepare your document in a drawing program such as PowerPoint, using a portrait rather than landscape layout. This approach will allow you to create your figures with minimal hassle but maintain the look of a document rather than a presentation.

Document length should be about 16-20 pages. Please take this number with a grain of salt, as we have not evaluated this particular assignment/format on this topic before. Though somewhat variable, typical section lengths (including both text and figures) might be:

• Title page: 1 page
• Abstract: 1 page
• Background and motivation: ~2 pages
• Data presentation and interpretation: ~10-14 pages
• Implications and future work: ~2 pages

The first page of the document should include an informative title and author information (section/color/names); the second page should include just an abstract. A typical context page will be enhanced by a supporting figure, though some might include only text. Context pages may include a mix of narrative text and bullets – whatever helps you express yourself most clearly and concisely. A typical data page should include a figure or two, each with associated caption, and a few bullet points/short blocks of text interpreting that piece of data. (Reminder: Your figure captions themselves should avoid interpretation.) More detailed suggestions for content (as opposed to style) are below.

Content Guidelines

Begin by reading the general guidelines for scientific writing. In particular, the sections on Title, Abstract, Figures, and Holistic View of Data are particularly applicable to this assignment.

A few prompts to get you started are below, but note that this list is not exhaustive and also that several elements could reasonably be included in either the data section or the conclusions section.

Background and motivation: guiding questions

Please include a few references in this section.

• What is the context of the study that you are presenting? Can you convince your reader that your specific study relates to broader questions or a bigger picture that this research might help clarify? In other words, why is this research interesting?
• For Module 1, you may wish to focus on the microbiome, the host/microbe relationship, ecology and host interaction with the environment, another aspect, or some combination of these topics that you think will intrigue your reader. Keep in mind, you have little space to motivate your work and you need to catch the reader’s attention.
• Are there some unanswered questions a step below the big picture that this type of work could help answer? What sort of result would be a clear step forward in understanding how microbial communities vary between birds of a different species or sex? Are there some types of changes that have been tested experimentally or examined in natural populations in prior studies that shed light on your expectations? Are human studies relevant to this work? Studies in poultry?
• As you bring the reader closer to your specific study, can you clearly and succinctly describe what aspects of the microbiota you have examined, and how you have applied this information to draw conclusions in your experiment/analysis?
• What were your expectations at the outset of the experiment? (Be sure you’ve clearly explained your hypothesis.) Would your introduction benefit from a brief summary of your (and the class’s as a whole) results? Do these contrast with your expectations?

Data: suggested figures and guiding questions

Throughout this section, you may focus first on your team sample (and associated 16 sequences), and then branch out to discussing the contributions of “[our] colleagues.” In the construction/experimental phase (PCR gel, cloning), you may focus mostly on your own samples and treat the class-wide samples briefly. In the evaluation/analysis phase, you should most thoroughly assess your own samples but also treat the class-wide samples in substantial detail. More guidance is provided below.

Note: Keep in mind that we will hold off on practicing a proper methods section until the second module. In this assignment, figure captions and/or supporting text should include only the most relevant aspects of the methods, such as the sample identities and analysis choices.

Experimental overview

• Schematic: Overall experimental plan and main steps involved

Recall that our collaboration and integrity guidelines state that your text and figures must be your own unless otherwise specified. Thus, you should all make your own schematic rather than modifying one from class slides or the wiki. Keep in mind that you are being evaluated not on advanced PowerPoint skills, but instead on showing that you understand the purpose and major steps of the experiment and can convey them. You may prepare something similar to schematics presented in class, but remember that your goal should be to make a figure tailored specifically to this assignment and audience. What elements might be cut or added? How can you modify the figure to best highlight key takeaways?

Preparatory phase of experiment

• Figure: Gel from initial PCR
• Potential schematic: Cloning plan

What was the purpose of any data you collected during this phase and what valuable information was established? Include the role of controls when applicable.

You can briefly establish DNA recovery and colony count results without belaboring them. (No huge tables needed.)

Analysis phase of experiment

The following tables/figures are required:

• Table: Species summary table for you and your partner’s samples (similar to Excel table that you made but more simple/including just the key elements)
• Figure: MEGA phylogenetic tree for each of 9 gulls (up to 24 sequences each)
  • one of these you have contributed to, and the rest are taken from the wiki as is
• Figure: Composite phylogenetic trees for each unique species/sex combination (3 trees total: male RBG, female RBG, male HG)

You may include other table(s) or figures that summarize interesting individual or class-wide findings, such as:

• Excerpt of your MEGA sequence alignment, such as an area with many substitutions
• Class-wide species table in some high-level form
• Composite tree comparisons across one parameter (e.g., in 2 trees: all male birds versus all female birds)
• Composite phylogenetic tree across all 9 gulls (1 tree total)
• UniFrac comparisons – this analysis requires re-doing the trees in MEGA to be rooted rather than unrooted, or otherwise adding a root, as only the former format is accepted by UniFrac
• Your brilliant idea here!

The guiding questions below may give you further ideas for developing both figures and associated text. Feel free to include a few references in this section if they are relevant to your claims.

• How might you highlight differences and similarities between bacterial species identities found in two or more distinct bird populations? Consider a Venn diagram.
• How might you highlight differencess and similarities between bacterial species frequencies found in two or more distinct bird populations? Consider a color-coded bar chart that depicts species frequency found in each population. Pie charts that show percent abundance could also be useful.
• For each composite (multi-gull) tree representing a given population, consider whether individual gull samples are evenly distributed among species and/or higher-level branches or not.
• How do the topologies of the trees differ, both intra-species and inter-species (or sex)? Consider how many major clusters each tree has and how far apart they are.
• If you create one comprehensive tree for all gulls, do you gain any further insights about the relatedness of bacteria in the different populations?
• What hypotheses can you present for why certain bacteria are shared among populations and why certain bacteria are unique to a specific population? What further experiments can you propose to test these hypotheses? Are the primary functions of any of these bacteria in the gut already known?
• Given the limitations of defining to the species level, what patterns (if any) do you see at higher order levels such as family or phyla? Can you think of possible specific reasons for these patterns related to the disparate environmental conditions for the two species (from two nearby but distinct locations) or sexes?
• What aspects of your data/findings might you expect to be different, and which the same, if the sample size were increased?

Implications and future work: guiding questions

Be sure to keep this section focused and brief – don’t lose your reader in speculation that is too wild or tangential. Some of the questions below can be addressed in just a couple of sentences, while others you may want to devote more time to. Overall, consider these prompts a starting point for your thinking rather than a set of boxes to check off.

• Your experiment in this module was focused on a specific question and hypothesis. Now let's return to the 'big picture' questions of disease ecology, some of which you may have introduced in the Background & Motivation section. Discuss the implications of your data in the context of disease ecology and suggest new questions that arise from your experiment.
• In some ways, our protocol for this experiment was constrained by the time we have to complete the module and to do an analysis, as well as by financial resources for the class. Are there ways you would suggest to improve the procedures while staying with the same general approach? Is there a different method that would be better if given the time and finances?
• Based on the results, whether they matched your expectations or not, what experiments would you want to follow-up with? Follow-up experiments could distinguish between competing explanations of a given outcome or broaden the sample set for a question you already asked, to give just two examples. What might be the most important thing to know next about this system? How might you investigate the reasons for some of the differences you observed?
• How might knowledge of the bacterial communities that you studied influence other areas of research that might be proposed with these same birds? Or more generally, how does knowledge about any animal’s gut bacterial community influence other areas of research? Do your findings have implications for wildlife management? Is there another system in which the same approach would be particularly useful?
• An ultimate outcome of this work would be the ability to describe the composition of the microbial community in a given animal/environment precisely, and then to understand why one differs from another. How might you apply this knowledge? Are there implications for public health or for an application that is not too far-fetched?