Annotated Bibliography Assignment
50 pts
This assignment is designed to help you find and evaluate primary literature as you learn about
a specific topic in the field of microbiology. An annotated bibliography is used to provide a
succinct overview of the available knowledge/research on a given topic. This helps researchers
discover gaps in the current literature, which informs decisions about future research projects.
An annotated bibliography typically includes a citation followed by a paragraph summarizing
and describing the source (details below).
Instructions:
1. Pick a topic that you find interesting in the field of microbiology. Use your textbook, current
interests, or a recent news article to help you pick an interesting topic. Remember, you will
be spending a good amount of time looking for and summarizing literature on this topic so
make sure you enjoy it.
2. Summarize your topic in a sentence or question.
a. Ex: The effect of wildlife crossing structures on the migration of long-toed
salamanders.
b. Ex: Is climate change affecting the population dynamics of endemic high elevation
salamanders?
3. Use a scholarly database to find relevant peer-reviewed research articles on your topic by
using keywords or phrases.
a. Ex: wildlife crossing structure AND long-toed salamander.
i. Note: If appropriate, don’t forget to use scientific names of species as well
(ex: Ambystoma macrodactylum)
b. Good databases for biology related articles include:
i. Google scholar: https://scholar.google.com/
ii. Scopus: Go to https://www.liberty.edu/library/databases/?l=S and select
“Scopus”
iii. EBSCO Quick Search: Go to, https://www.liberty.edu/library/databases/?l=E
and select “EBSCO Quick Search”
iv. ProQuest Biology Database: Go to
https://www.liberty.edu/library/databases/?l=P and select “ProQuest Biology
Database”
c. If you don’t understand what a primary research article is, please use this tutorial:
http://libguides.ius.edu/c.php?g=363002&p=2452829. Using articles other than a
primary research article will result in point deductions
d. Important notes:
i. Library resources (some links above and access to full-text articles) may not
be available off campus.
ii. If the full-text of an article that you would like to use is not available from our
library, you can submit an interlibrary loan request.
https://www.liberty.edu/library/interlibrary-loan-residential-students/
iii. While searching, select an option to only include peer-reviewed articles
(available on EBSCO and ProQuest).
4. Review the current literature on your topic and pick 4 primary research articles. These
articles should be original research (NOT review articles) relevant to your topic. Write a
citation for each using the format below. Order the citations in alphabetical order according
to the first author’s last name.
Author 1 last name & initials, Author 2 last name & initials, etc. Year. Title of article. Journal
Name Italicized Volume of journal bolded: page numbers or DOI.
Pagnucco KS, Paszkowski CA, Scrimgeour GJ. 2012. Characterizing movement patterns and
spatio-temporal use of under-road tunnels by long-toed salamanders in Waterton Lakes
National Park, Canada. Copeia 2: 331-340.
*Note: if more than 7 authors use “et al.” (example: Goober AJ et al.)
5. For each research articles, write a summary of the study in your own words. The summary
should be a 300-400 word descriptive and evaluative paragraph of the article. Remember,
you are writing a summary of the article, not an essay. Also, the summary is NOT a
paraphrase of the abstract, but is your review of the article. Your summary should include
the following items. Please denote each item in the paragraph as shown in the example
posted on Canvas.
a. Hypothesis(es)/objective(s) of the study
b. Key finding(s)/result(s)
c. Evaluation of methods and/or experimental design used as it relates to the key
findings. In other words, what could be improved about the study OR were all the
methods used in the study satisfactory and why?
d. Significance of the key findings as a contribution to your question/topic. In other
words, what is the take home message as it relates to your interests/topic?
e. Does this study spark ideas for future research studies? OR Do the key findings
contradict previous research, explain?
*Do not use direct quotes in your summary. Everything should be in your own words.*
Javan GT, Finley SJ, Smith T, Miller J, Wilkinson JE. 2017. Cadaver Thanatomicrobiome
Signatures: The Ubiquitous Nature of Clostridium Species in Human Decomposition.
Frontiers in Microbiology 8:10.3389/fmicb.2017.02096
Summary: a) In the research article named “Cadaver Thanatomicrobiome Signatures: The
Ubiquitous Nature of Clostridium Species in Human Decomposition” the objective is to
study the impact of the 16S rRNA gene hypervariable region selection in differentiating
thanatomicrobiomic profiles to produce empirical data to understand the Postmortem
Clostridium Effect. b) The results of the study concur that methane produced during
decomposition along with other various putrefaction gases is a necessary component of
survival for these bacterial taxon through the use of 16S rRNA gene V3-4 combined regions.
Additionally, Escherichia coli, Clostridium septicum, and Pseudomonas sp. were detected
using both regions that were only in the female cadavers. c) Due to the results of the study, it
should be noted exactly how many cadavers were female so that in a future study the male
and female numbers could be even due to the varying results found between genders. The
findings of the study also left much to be discovered due to the post results not identifying id
the hypervariable regions could potentially discriminate all bacterial species. This, however,
cannot be proven without further testing. d) The findings of this study note that the microbial
present in the liver and spleen of the cadavers use the gases formed during the putrefaction of
the body to survive. The Clostridium species present have the ability to digest the vertebrate
collagen fibers that breach the colons epithelial tissue and mucosal layers. e) This study
sparked the idea to do a study that analyses the presence of the different types of microbial
populations in the liver, the organ with the most microbial population, and the heart, which is
the center of blood flow. This is because of the ability of Clostridium to develop via the
cessation of the heart creating the possibility of very different microbial population in these
organs.
Ashe, EC, Comeau AM, Zejdlik K, O’Connell SP. 2021. Characterization of Bacterial
Community Dynamics of the Human Mouth Throughout Decomposition via Metagenomic,
Metatranscriptomic, and Culturing Techniques. Frontiers in Microbiology 12:
0.3389/fmicb.2021.689493
Summary: a) The study was conducted to determine the existence of a “microbial clock”
through the use of the human hard palate and the microbes present at different stages of
decomposition. b) The results of the study concluded that there was no apparent correlation
between the length of the postmortem interval and the bacterial community present at a given
time. c) There were a few variables in the study that could be improved upon including the
humidity, temperature, sample size, cause of death, donor sex, weight, and scavenger activity.
These variables caused a potential fluctuation in the results that could not be analyzed
without the help of another experiment to provide more accurate results. The normal human
oral microbe swabbed before death, did eventually lead to other genera as time passed
showing that it could be possible that different microbes appear during different times of
decomposition. There was a difference between the live verse fresh samples, but due to the
fine resolution required to indicate the postmortem interval the results were not a clear
source. d) The findings are relevant to my topic because it is important to note that while a lot
of the microbes in your body do have an effect on decomposition there are also many that do
not. This research, in specific, also mentions the “microbial clock” which is essential to
understanding the functions of microbes during decomposition and when they are present
during its various stages. e) The results of this study spark many new ideas on ways to
advance the study of the postmortem microbiome by creating a way to narrow down and
specify the differences in the various microbial organisms present in the body right before
death and throughout various points during the five stages of decomposition. This research
would allow for the establishment of the “microbial clock” as a real device to support the
postmortem interval.
Schoenen D, Schoenen H. 2013. Adipocere Formation- The Result of Insufficient Microbial
Degradation. Forensic Science International 226: 10.1016/j.forsciint.2013.01.023
Summary: a) The process of decomposition of human tissues is aided by microbials. When
the microbial population is disrupted during their aid in decomposition, the end formation is
adipocere due to oxygen deprivation. b) The results of the study concluded that all of the
organic substances relative to a human corpse’s tissue can be degraded by respiration, while
the internal aspects require fermentation and cannot be completely degraded. Due to the
inability to fully breakdown fatty acids, the microorganisms convert them to polyhydroxy
fatty acids which eventually lead to the formation of adipocere. These fatty acids, however,
are not a long-term solution for the stability of adipocere. The microorganisms use adipocere
as a storage substance of the excess organic materials, but do not provide it with any means
necessary to metabolize because microorganisms cannot produce triglyceride. When oxygen
is present adipocere is not formed due to all the organic substances that make it up being
degraded. c) All of the methods in the study were satisfactory for their intended purpose to
accurately show the different requirements of microorganisms in decomposition. The
breakdown and analyzation of the components forming the organic substances and the
process for degradation and fermentation helps to explain the research better for readers. d)
The findings comprised by this research are relevant to my topic because they explain the
process of microorganism degrading the human tissue and internal structures through
respiration and fermentation, respectively, and how these factors affect the rate of
decomposition of a human corpse. Both of these processes affect decomposition and are vital
to include. e) This study sparks the idea to do research on the reasons behind the stability of
adipocere through the use of biomedical pathways and other environmental influences to
microbial activities. When these factors are taken into account the study can provide
adequate results relevant to how microorganisms affect human decomposition.
Cobaugh KL, Schaeffer SM, DeBruyn JM. 2015. Functional and Structural Succession of Soil
Microbial Communities below Decomposing Human Cadavers. PLoS ONE 10: e0130201.
doi:10.1371/ journal.pone.0130201
Summary: a)The study focuses on the use of microbial communities in soil decomposing
human-derived organic matter and identifies putative predictor populations for postmortem
interval estimations. b) The results of the study noted that when cadavers decompose on the
surface of the soil it causes changes to the soil itself, and the microbial populations that live
there. Structural and functional changes occur underneath the soil of decomposing cadavers
which is exponentially increased during the Active Decay stage. It is also noted that these
microbes that interact with the soil from the remains last for a longer period of time
suggesting their advanced role in decomposition. c) All the methods in the study were
satisfactory in providing results consistent with the expected outcome through careful and
methodical procedures. d) The results from the research are relevant to my topic because it
proves that the human body does use microbes to help with it its decomposition and that
these microbes are also useful for enhancing the soil in its decomposition methods. The
article also touches on the use of these bacterial communities inside and on the body in
predicting the time since death. e) A study that could be done to improve upon the
information learned would be to study the microflora that remains in the soil after
decomposition and its role in the ecosystem as it relates to the microbes already present in the
soil and their role in decomposition.
Please type the requested information above and then submit a word file on Canvas and
hand in a hard copy by the due date listed on the syllabus. Also include a blank grade
sheet (on Canvas) stapled at the end of your bibliography – failure to follow these
instructions will result in a 5% grade deduction.
Grades will be based on the following: pts
Correct bibliography format 4
oCitations in alphabetical order (1 pt)
oSummary items denoted in text (ex: (a), (b), etc.) (1 pt)
oSpelling/grammar (2 pt)
Microbiology topic stated and well written in sentence format. 2
4 relevant citations, 1 pt each 4
oFollowed correct citation format (0.5 pt)
oPrimary research article relevant to topic (0.5 pt)
4 article summaries in paragraph format, 10 pts each 40
o2 pts for each well written summary item
Powered by TCPDF (www.tcpdf.org)
