A Guide to Writing Research Papers for Introductory Microbiology
A research paper is a report of original research and is, without doubt, one of the most important documents written by scientists. Research papers communicate important findings and ideas to other scientists, especially those working in the same or similar fields. In turn, they are given the opportunity to evaluate, revise and extend the research you have communicated. One of the important components of this course is to train you on how to conduct research and communicate your findings in the form of a professionally produced research paper. You will be carrying two research projects during the semester. One will involve the isolation and characterization of a particular microbe or microbes, the other focuses on various aspects of antibiotic drug resistance. The research papers you will be required to write follow a format common to most journals dedicated to the biological sciences. The format given below conforms to that stipulated by many biological journals. The format is broadly based upon that required for full research papers in The Journal of Bacteriology, published by the American Society of Microbiology.
Manuscripts should be written in concise and grammatically correct American-English, and must be submitted according to the format specified below. The manuscript should be typed, the lines double-spaced, and one inch margins reserved on either side of the page. All titles should be bold and centered. Each section should begin on a new page. Typically, the paper will consist of seven sections: The Title page: a descriptive title of the article, the name of the author, and her/his departmental and university affiliation, and e-mail address for correspondence. The Abstract: a short narrative that summarizes the major accomplishments of the work being described. An Introduction: a statement placing the work to follow in historical perspective and explaining its intent and significance. Materials and Methods that describes how the research was conducted so that it can be repeated by other investigators. The Results section describes and analyzes the experimental data. The Discussion explains the interpretation of the results and their significance. References documents all the sources consulted in carrying out the research and writing the paper, and Figures and Tables which illustrate the major data as photographs, graphs and tables.
Writing research papers is a very difficult enterprise, so do not expect to become an expert straight away. Familiarize yourself with the style of research papers by carefully studying published material: you will be given ample opportunity to do this during the course. You do not have to aspire to the professional level of these papers. However, you must pay careful attention to the content and style of the papers. Bear in mind that the papers you consult reflect many weeks, or months of intensive research, and your research projects will only last a few weeks. Therefore, the audience for your papers will be your peers and instructors. You will, in fact, be given the opportunity to review and evaluate papers submitted by your peers during the semester. The guide below is based upon these premises while at the same time reflecting the requirements for professional journals. Excerpts (edited for anonymity) included here are from previous student papers and sample papers prepared by students in previous years will be posted on Blackboard.
TITLE
The title identifies the work accomplished and should be descriptive rather than vague and immediately inform the reader about the work you are about to describe. Also include on the title page your full name, your affiliation (in most cases, this will be the Department of Biological Sciences, the George Washington University), a contact address (which nowadays is an email address) and the date of submission on the manuscript. The title should be informative and specific and accurately indicate the major focus of your work. For example, a title: “The Isolation of Bacteria from Raw and Cooked Food Samples” is too general and unfocused. A more descriptive title is: “A Quantitative Study of Fecal Coliforms Found in Cooked and Raw Samples of Minced Beef.”
Similarly, a paper that is titled: “Isolation of Staphylococcus aureus From Swimming Pools” is best replaced by a title that reflects the research more specifically: “Isolation and Characterization of Chlorine-Resistant Staphylococcus aureus from the Recreational Indoor Swimming Pool in the Lerner Health Center of the George Washington University.”
The title may also reflect the major finding of the research: “Halobacterium Species Isolated from Salt Water Marshes near the Patapsco River Estuary of the Chesapeake Bay.”
Bear in mind that with the large number of research papers published each month, indexing services rely heavily on the titles of papers, as do scientists scanning the literature for papers pertinent to their own fields of research.
ABSTRACT
The Abstract is a summary of the major points of the paper, including the purpose of the research, the methods used, the results obtained, and the conclusions drawn from them. The Abstract typically consists of a single paragraph of about three hundred words. It should be borne in minds that, together with the Title, the Abstract will be read by many people who may not necessarily read the rest of the paper. Therefore, this section of the paper must stand on its own. It is also the most difficult part of the paper to write because you must summarize, in a short space, the entire scope of your project. The excerpt below reflects a typical first draft, followed by an acceptable revision.
Example 1: First Draft
“Cell phones may harbor all kinds of bacteria and the purpose of this study was to isolate Staphylococcus aureus, a potentially pathogenic microbe. Several cell phones were employed in this study. The phones were swabbed and S, aureus isolated by growth on mannitol salts agar plates. A number of techniques were used to test the colonies. The resultant colonies were tested by gram-staining, for mannitol fermentation, and oxidase and catalase activity to confirm the isolation of S. aureus. Several isolates were then tested for antibiotic resistance using methicillin, ampicillin and penicillin. About 40% of the isolates tested positive for methicillin resistance and 20% were found to be resistant to ampicillin and penicillin. These results indicate that cell phones may be a source of potentially pathogenic, and antibiotic-resistance bacteria, and may well pose a significant public health threat.”
This example presents an interesting study but the Abstract is unfocused and vague. Why were cell phones chosen in particular for this study? How many cell phones were tested and how many were found to be contaminated with S. aureus? Why was mannitol salts agar used as the selective medium? The sentence, “A number of techniques were used to test the colonies” is superfluous and should have been removed. Although the analytical tests are indicated, the results are not. The author should have stated these precisely in order to convince the reader that S. aureus strains were, in fact, isolated. The studies on the antibiotic resistances of the isolates unnecessarily are presented in a vague manner. Again, the author should have briefly justified why these particular antibiotics were chosen and given the actual numbers of isolates that were tested and found to be resistant to different antibiotics as well as the percentages. Finally, the last sentence is too dramatic and not warranted based upon this present study. A more conservative conclusion is called for. All these points are reflected in the revision:
Example 2: Revised Abstract
“Over the past decade, advances in cellular technology have contributed to increases in cell phone usage. Cellular devices have become an integral form of communication and are used by over 23 million people worldwide. Phone conversations, text messaging, and emailing, are all behaviors associated with cell phone use, and require the skin to be in contact with these devices. We hypothesized that cell phones may harbor Staphylococcus aureus. S. aureus is a bacterium that inhabits human skin. Certain strains of S. aureus are capable of causing disease and some are antibiotic-resistant. In an effort to determine if S. aureus was associated with cell phones, sterile swab samples were collected from twelve different phones (flip and non-flip styles) and plated onto mannitol salts agar medium which is recommended for the isolation and identification of S. aureus. Putative S. aureus colonies were obtained from all the phones tested. 192 out of 200 colonies tested positive for mannitol fermentation and were characterized further. All bacteria were gram positive, aggregated cocci and tested positive for oxidase and negative for catalase, confirming the isolation of S.aureus by Bergey’s criteria. Previous studies have shown that many S. aureus strains have developed resistance to the β-lactam class of antibiotics. Therefore, 40 randomly selected isolates were tested for resistance to three β-lactam antibiotics, methicillin, ampicillin and penicillin, widely used in medicine. Results from the Kirby Bauer procedure suggested that 16 (40%) of the isolates were methicillin-resistant and 8 (20%) were additionally resistant to both ampicillin and penicillin. The results of this investigation suggest that cell phones may pose public health concerns.
This version of the Abstract is much better. It begins by stating the problem and justifying the research. Results rather than procedures are emphasized. The hypothesis is clearly stated and the major data clearly presented, substantiating the isolation of antibiotic-resistant S. aureus and lending credence to the author’s hypothesis. Note, too, that the Abstract is written in the past tense, and abbreviations, literature citations and figures are not present.
INTRODUCTION
The Introduction provides a framework for the paper including a background (which is often in the form of a literature review) of the topic, and the purpose of the work. This section should be neither too broad nor too narrow. There is no specific length requirement but generally this section can be written in two main paragraphs. The first paragraph should summarize prior research in the area that you have studied. Do not provide a detailed and extensive literature review but instead confine the background information to what is strictly relevant to the work you’ve undertaken. Be sure to indicate references in the text (this will be discussed later). This paragraph must be written in the past tense. In the next paragraph, describe the unique aspects of your work (written in the present or, as appropriate, the future tense); that is to say, provide a justification (and a hypothesis) for the work you’ve carried out. For example, how does your research contribute to the studies undertaken by previous authors? What new information is your research attempting to discover and clarify? You may also briefly preview some of the results in order to lend credence to the importance of your study. Since your paper will be evaluated by your peers and the instructors, the scope of the introduction should be aimed at this audience.
You must follow the conventions of the International Union of Microbiological Societies (http://www.iums.org) in naming bacterial species. The convention specifies that binomial names of species must be used and underlined or italicized in the text. When a microbe is first named, its full genus and species name must be written; thereafter, the genus name can be abbreviated. Thus, the species Pseudomonas fluorescens must be stated in full when first introduced, but afterwards shortened to P. flourescens. Do not confuse proper nouns with common nouns. P. fluorescens is a particular species, but the term pseudomonads (which is not italicized) refers to many of these species. Similarly, staphylococci are a wide range of bacteria that exhibit a similar shape and aggregation, whereas Staphylococcus is a particular genus that exhibits these properties.
MATERIALS AND METHODS
This section provides the information which will enable other researchers to reproduce the experiments you have carried out. It describes the procedures you used to conduct your research, the controls you incorporated and the means by which you evaluated your data. It is important to be precise. The materials and procedures you carried out lend credibility to your scientific arguments presented later. Similar experiments carried out by others may not always yield the same conclusions, reflecting, perhaps, different interpretations of the data. In addition, this section will provide critical information to others who may be working on similar research and may need to use experimental approaches and techniques similar to the one you employed. Throughout, use the past tense.
Make sure that you organize the description of experiments logically and methodically, in the order that they were performed. It is helpful to organize this section into subheadings, beginning with a description of the materials used in the project. This makes the text easier to write and makes it more understandable, and easier to follow, for the reader. You do not need to provide an extensive list of all the materials you used, such as Petri dishes, gram stain reagent kits, and other common purpose items. You simply state that all chemicals and apparatuses “were provided by the Department of Biological Sciences, the George Washington University”. However, you must relate carefully the sources of your specimens, how they were collected and under what conditions. In addition, if you used standard bacterial strains in your study, these must be described and their sources noted. When describing the methods you used, again be precise, but not over-descriptive. Common microbiological techniques, such as Gram staining, oxidase testing, etc., do not need to be described but simply referenced in the text (usually, you will cite the laboratory manuals). It is necessary, however, to emphasize the purpose for using particular procedures, but be careful not to describe any results until the next section.
Avoid common grammatical errors which often pop up in this section. Media (not mediums) is the plural of medium; datum (singular) should not be confused with data (plural). Never use phrases such as, “The S. epidermidis-containing cultures were…” when you mean “The samples containing S. epidermidis were…” Surely, you would never write, “The coffee-containing cup was…”?
RESULTS
This section presents the data you accumulated in the course of the study. Once more, the narrative must be in the past tense. Before writing this section, it is advisable that you first construct the tables and figures you will be presenting in the text (see later). Be sure to reference each table and figure in the text (as Table 1, Figure 2, etc.) In the text, it is best to summarize the data and point out important facts and trends; the details can be included in the tables and figures. In order to present the data effectively, this section must be well-organized, preferably in the sequence in which you described your methods. Since many projects will involve the isolation of novel microorganisms, you should carefully designate each isolate, preferably using letters and/or numbers, as follows: “Two isolates, chosen for further characterization, were designated GH104 and KJ106. The characteristics of both strains are summarized in Table 3. After describing the characteristics of a particular isolate, you can then propose a putative identification. Thus, “Isolate HG411 was found to be a large Gram-positive motile bacillus, often occurring in short chains. It was non-fermentative and tested negative for nitrate reductase. It did not grow in anaerobic medium leading us to hypothesize that it was an obligate aerobe. This was substantiated by positive results for both oxidase and catalase activities. In addition, the presence of clearly defined endospores, shown by malachite green staining, led to the tentative identification of HG411 as Bacillus cereus.” Note that the author is careful to point out that this is only a tentative identification. It would take many more weeks of experimentation, probably using determinative tests unavailable to us, to confirm this deduction. Of course, these further tests can, and should, be described in the Discussion
When writing the Results (and Discussion), do so in a direct, straightforward manner. Use the past tense. The use of simple and effective prose is more likely to convey your ideas to the reader (the excerpt above is an excellent example of this kind of writing). Use short sentences. One of the most common errors in writing papers is a tendency to wordiness and the use of jargon. Most jargon is long-winded and confusing, employing words that are unfamiliar to a general reader and this can change what should be an interesting paper into one that is tedious and even boring to read. In fact, it often has the effect of alienating rather than engaging the reader. In addition, you are encouraged to avoid wordiness and the use of redundant phrases. Common modifiers such as “very, “rather” and “quite” are unnecessary and should not be used. Other common examples of wordiness, and how they might be corrected, are given below. Note that simple direct phrases and sentences have a clear and confident tone.
The results would seem to indicate…. The results indicated….
Due to the fact that…. Because….
It may be that…. Perhaps….
A further piece of evidence that pointed…. Further evidence was….
The following day, after 24 hours of incubation, Colonial growth was observed after 24 the plates were removed from the incubator hours of incubation. and observed.
The data indicated that strain AB14 was a Gram- Strain AB14 was a Gram-negative bacillus. bacillus.
Many writers are torn between whether they should write the paper in the active or passive voice. In the former, the subject performs the action; in the latter, the subject receives the action. Too much use of the active voice has the tendency to make the text monotonous because of too many first-person references. On the other hand, overuse of the passive voice can cause the tone of the paper to be dry, boring and even pompous. To ensure that the text is more lively and readable, it is best to try and strike a balance. Consider the following example:
“We used eosin-methylene blue agar plates for the preliminary isolation of P. aeruginosa. The bacteria were Gram-negative bacilli, and motile. The results for oxidase and catalase activities were negative. Additional experiments showed that the bacteria did not ferment glucose, galactose, maltose or lactose (Table 2). Based on these results, we concluded that the organism had an oxidative metabolism.
Try translating this in to an entirely passive or active tone. You’ll notice that the creative mix of both voices makes this narrative not only lively and engaging but also states the results in a clear, confident and unambiguous manner.
DISCUSSION
In this section, you will interpret the results in the context of the questions and hypothesis you explicated in the Introduction, as well as addressing broader issues that were raised by your research. Before you begin, consider the issues raised by your results. Were they the results you expected? Did they support your hypothesis or not? If they did, your Discussion will be brief: if they did not, then you must consider alternative explanations. How might you address any unexpected results in future research? What future directions might this research follow? Finally, what are the scientific and/or public health implications of your research? It is important that you draw your conclusions from the data you obtained and relate them to previously published work (which, of course, must be cited). Your results may be open to many interpretations, but only you can decide which one(s) are the most significant.
It is essential that the text convey confidence in your results and conclusions. Avoid ambiguity and uncertainty. For example, consider the extract below:
“Our analysis of Georgetown Canal water samples showed that E. coli was present in excess of 103 cfu/ml; however, quantitative data on other coliform bacteria were not completed. This study must, therefore, be considered only as a preliminary study.”
The statement, although strong to begin with, ends on an evasive and inconclusive note that leads the reader to doubt the author’s belief in her own research. An acceptable revision would read as follows:
Our analysis of the Georgetown canal water samples showed that E. coli was greater than 103 cfu/ml. The presence of other coliform bacteria was not investigated but our results clearly indicate that the fecal contamination of the canal is in excess of city standards for public health (reference). In view of these results, we propose that further investigation on the canal be carried out.
This narrative is much more confident. It emphasizes the results and points to their significance, and the reader, in return, is assured of the author’s credibility. Furthermore, the author’s proposal for future research, asserted by these bold statements, appears authoritative, logical and fully justified.
REFERENCES
Documenting your paper thoroughly is a hallmark of good scientific writing. Any ideas or results which are not your own must be cited at the appropriate places. Cite sources in the text using the format recommended by the Council of Science Editors (CSE: www.councilscienceeditors.org), often referred to as the name-year system (this is different from the format specified by the Journal of Bacteriology). For example, “Staphyococcus aureus is a Gram-positive coccus, widespread in nature, which has been implicated in a number of human and animal diseases (Tolura, 2008)” or “Shimkets and Dworkin (1998) point out that many Myxococcus species…” or “Water samples were evaluated for E. coli contamination following the procedure described by Nathan (2002).” You do not need to repeat the citation for every sentence attributable to a particular source. However, if you are discussing the work at some length it is advisable to cite the reference at the beginning and the end of the paragraph to indicate that you are still referring to the same source. Do not reference general material that is widely known. For your major sources, you may include your textbook, laboratory manuals, published research and review papers and class handouts. If one or more of your sources is attributable to word of mouth (a discussion with the instructor, for example) then indicate this in the text as “(Morris, DW, personal communication).” This is not repeated in the References section. Use quotations from other authors only sparingly in the text when you need to emphasize a particularly significant aspect that has drawn wide attention.
Sources in the References section can be ordered as they appear in the text or alphabetically. Common examples are given below.
Book
Tolura, GM. 2006. Microbiology. 4th ed. San Francisco: WH Freeman. 670 p.
Article or Chapter in an Edited Book
Shimkets, LM, Dworkin, M. 1998. The Myxobacteria. In: Shapiro, JM, Dworkin, M. editors. Bacteria as Multicellular Organisms. Oxford: Blackwell Scientific. p. 121-145.
Journal Article with a Single Author
Neu, H. 1992.. The Crisis in antibiotic resistance. Science. 306: 1064-1073.
Journal Article with Two or More Authors
Chanishvili, N, Chanishvili, T, Tediashvili, NM, Barrow , PA. 2001. Phages and their application against drug-resistant bacteria”. J. Chem. Technol. 36: 192-198.
Web Site
District of Columbia Water and Sewer Authority (2000). Facilities: Water Treatment. Retrieved October 29, 2008, from DC Water and Sewer Authority Web site: https://www.dcwater.com/
Course Handouts or Laboratory Manuals
Morris, DW. 2008. Biological Sciences 137 Laboratory Manual: The George Washington University. 112 p.
TABLES AND FIGURES
Most scientific papers are supplemented with tables and figures that summarize and present essential data that convey information more effectively than the text. All must be of high quality. When you begin to construct your tables and figures, you must decide how you are going to depict your data most effectively. Is a graph more effective than a table? Do you need both? You must ultimately decide how best to display your data so that it is a convincing argument for your hypothesis and emphasizes the major findings of you research. When you have made your tables and figures, number them consecutively in the order they are referred to in the text. Each should have a title and a brief descriptive legend. It is important that each table and figure stand on its own and still be understandable to the reader.
A common fault beginners make is to include all their data in the form of tables and figures. However, this is unnecessary and in some instances, data can be more easily and more effectively summarized in the text. Tables and figures must include only selective and important data. For example, the table below reflects uniform data and is unnecessary. The data may be explained more concisely in the text as, “All three strains (NM 102 – 104), originally isolated on mannitol salts agar, were found to be non-motile gram-positive staphylococci and tested positive for catalase and negative for oxidase.” Tables must display more variable data. The examples in your laboratory manuals contain many good examples.
Table 2: Morphological and Physiological Characteristics of Thee Independent Clones Isolated on Mannitol Salts Agar.
|
Strain |
Cell Shape |
Aggregation |
Gram1 |
Motility |
Catalase2 |
Oxidase2 |
|
NS 102 |
Coccus |
Grape-like clusters |
+ |
Non-motile |
+ |
– |
|
NS 103 |
Coccus |
Grape-like clusters |
+ |
Non-motile |
+ |
– |
|
NS104 |
Coccus |
Grape-like clusters |
+ |
Non-motile |
+ |
– |
Key: 1 + indicates a gram positive reaction; – indicates a gram negative reaction. 2+ indicates a positive reaction; – indicates no reaction.
Similarly, photographs or drawings of microbial cells can be omitted and described in the text, unless you are pointing out important features on the illustration. If you present graphs, clearly label each axis. Do not be tempted to provide a graph and a table of the same data: one or the other is sufficient.
DRAFTING AND REVISING
You can expect to produce several drafts of your paper before it is ready for submission. Before you begin, study the instructions for the paper format carefully so that your paper is organized properly from the beginning. In fact, for the first draft, you should concentrate on the content and organization of the paper, and write down all of the information that you wish to include in the paper. Later, you can focus on style, grammar and punctuation. Start with the easiest writing rather than at the beginning. I find that writing the Materials and Methods first is best and it can usually be commenced before the project is finished. Alternatively, you may want to start with the Introduction since much of this can be adapted from your proposal. Be sure to prepare the Tables and Figures before you start writing the Results and Discussion sections. Generally, it is best to write the Abstract last of all, once all of the other sections of the paper have been completed. Be sure the follow the guidelines outline above.
I have found that there is a marked tendency for many beginning writers, lacking confidence in the power of their own prose, to rely on the quotations of other authors when wishing to make important points. This does not necessarily enhance the text and can, in fact, cause the reader to doubt the originality of the paper. It is perfectly permissible to paraphrase carefully material from other authors’ papers as long as the sources are cited. However, if you determine that a quotation will emphasize a particular point you are making, keep it short. A representative example is: “Baker (2007) describes Campylobacter jejunii as the ‘major causative agent of food poisoning deaths among children under five years of age in the U.S.’ His experimental data indicated that at least 67% of reported food poisoning cases were due to this organism.” The carefully selected quotation, enclosed within the author’s own text, emphasizes, and adds veracity to, the point the author wants to make.
Once you have written the first draft, go through the paper and check that is correctly formatted before you begin revising the text. Pay careful attention to grammar and punctuation. If you have a spell checker on your word processing program, by all means use it, but do not rely on it to detect all errors: these can only be spotted by carefully reading the draft. Proofreading can be tedious, especially if you have spent many hours writing the drafts. However, it is a task that must be performed with the utmost care. I have found that the best way to spot mistakes is to read the paper aloud, either to yourself or someone else. This practice will also enable to revise sentences that are unduly long or drawn out.
Research Proposal
The research proposal has much in common with the research paper. The proposal asks a question or poses a hypothesis that can be tested experimentally. There is no standard format for proposals, but it is important to conform to the guidelines laid down by the funding agency or organization. Your proposal must adhere to the format given below. The text must be double-spaced and include one-inch margins either side. Refer to Blackboard for sample proposals. The proposal must consist of five sections, beginning with a descriptive Title. The Introduction presents a review of the literature pertinent to the proposed research and leads to Research Aims which explicitly states the research question being asked and outlines its significance. The Methods section outlines your experimental strategy and, finally, the References section records your sources for the proposal.
TITLE PAGE
A full title of the project, your departmental affiliation and the due date for submission of the proposal should be presented on a single page. You will be working in groups of two or three but each individual must submit her/his proposal independently. The title, as with the research paper, must be specific and informative. The author’s name, affiliation and the submission date must also appear on this page.
INTRODUCTION
Background information (that is, a brief review of the literature concerning the topic of your proposal) should be presented in this section. To do a good job, you must read the literature carefully and selectively. Be aware of who you are writing for: in this case it will be your instructor and must, therefore, be scientifically accurate. This section should conclude with a short paragraph that states the research problem to be addressed by your proposal.
RESEARCH AIMS
The next two sections must be written in the future tense. In this section, clearly state the research objectives of your proposal. It is essential that you justify the aims of the proposal. How will it enlarge, clarify or disprove existing knowledge. What makes your proposal unique? Make your arguments convincing, citing references if appropriate. Try to predict the outcome(s) of your research. Finally, is the proposal adequate to address the research problem you have posed, or is it a preliminary investigation? Remember, you only have three weeks in which to carry out the research so you must be realistic about what you can accomplish in this short time.
METHODS
Describe the experiments to be conducted and the order in which they will be carried out. If you expect problems or ambiguities to arise, how would you explain or solve them? A detailed description of each experimental step need not be given (procedures for common microbiological techniques, such as Gram staining for example, should not be detailed at all) as long as the procedures are referenced and you explain why you are using this strategy. Point out the kinds of data you expect to generate and how you would evaluate and interpret it. Finally, be careful to explain how the data would support your hypothesis.
REFERENCES
References should be indicated in the text and cited in this section in the name-year manner as in the research paper.
RESOURCES
The WID Studio is a primary source of help and students are encouraged to use this facility. Two recent and helpful books on writing in the biological sciences are also available:
McMillan, VE. 2006. Writing Papers in the Biological Sciences. 4th ed. Boston: Bedford/St.Martins. 269 p.
Pechenik, JA. 2007 A Short Guide to Writing about Biology. 6th ed. New York: Pearson Longman. 281 p.