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Bibliography

The following is an annotated bibliography of literature used as sources for the


thesis. It is divided into three sections. The first section includes all primary sources.
These are all peer-reviewed papers published in accredited scientific journals. They
represent the bulk of the sources used. The second section also contains peer-reviewed
papers. These were used as supporting references for concepts presented in the main
references and as references for minor concepts presented to support the topic of the
thesis. The third section constitutes a list of agencies and websites used in the early
stages of research to formulate ideas. These are not cited in the text.
Primary Sources
1. Samuel, Buck S., et al. Effects of the gut microbiota on host adiposity are modulated
by the short-chain fatty-acid binding G-protein-coupled receptor, Gpr41. PNAS.
2008; 105 (43): 16767-16772.
The paper describes the study completed on the effects of microbes present in
mice guts in the regulation of body fat content. Microbes present in the mammalian gut
are responsible for allowing their hosts to absorb calories from otherwise indigestible
carbohydrates. When these carbohydrates are broken down short-chain fatty-acids
(SCFA) are produced. These acids are a ligand for the G protein-coupled receptor Gpr41
present in the gut. When there are less functioning Gpr41 (through a lack of SCFAs)
present in the gut there is also a deficiency of the hormone PYY whose function is to
increase time in the intestines to increase caloric absorption. Gpr41 deficiency is
therefore related to a faster intestinal transit rate and decreased calorie absorption.

Because Gpr41 function is dependent on the presence of the gut microbiotas ability to
ferment carbohydrates into SCFAs, mice without microbes in the intestine exhibited
Gpr41 deficiency and lower body weights. This paper illustrates the importance of gut
microbiota in regulating caloric absorption and therefore body weight.
2. Gordon, Jeffrey I. Characterizing a model human gut microbiota composed of
members of its two dominant bacterial phyla. PNAS 2009; 106 (14): 58595864.
The two major bacterial components of the human gut microbiota, the
Bacteroidetes and the Firmicutes, are discussed. A simplified model of the human gut
microflora was created by colonizing germ-free mice with B. thetaiotaomicron (a
member of the Bacteroidetes) and E. rectale (a member of the Firmicutes). This
simplified microbiota was studied to discover genomic differences and functional
differences between the two groups of bacteria. Interactions between the two groups of
bacteria were also found. When there was increased biodiversity (adding more E.
rectale) in the gut, B. thetaiotaomicron altered their gene expression to use glycans as a
source of nutrients that the other bacteria were unable to use allowing them to access
nutrients E. rectale could not. However, evidence shows that E. rectale alters its gene
expression in the presence of B. thetaiotaomicron in a way that allows it to better access
nutrients. Interactions between the two bacterial groups in such a way maintains a stable
ecosystem inside the mammalian gut.

3. Mikelsaar, Marika, and Mihkel Zilmer. Lactobacillus fermentum ME-3- an


antimicrobial and antioxidant probiotic. Microbial Ecology in Health and
Disease 2009: 1-27.
In this paper, Mikelsaar and Zilmer discuss the discovery of the bacteria L.
fermentum derived from the human gut. Bacteria exist within the gut microbiota that
have a number of important functions, the specific bacteria being an example of just one
of them. They show the benefits associated with the bacteria and the means by which
they discovered them. This study has shown how L. fermentum functions as an antipathogenic agent against disease caused by bacterial pathogens (such as Salmonella,
Enterococci, and Staphylococcus) and as an antioxidant. The bacteria inhibit the growth
of pathogenic bacteria through competition. It also helps to alleviate inflammation
stemming from the actions of free-radical oxygen.
4. Ruby, Edward G. Symbiotic conversations are revealed under genetic interrogation.
Nature Reviews Microbiology 2008; 6: 752-762.
Ruby outlines a variety of beneficial symbioses between bacteria and higherlevel hosts. Relationships described include the bacteria Vibrio living in the light organ
of the bioluminescent squid allowing the luminescence to be used in social interactions
with other squid. The role of Xenorhabdus bacteria in Steinernema nematode worms and
Photorhabdus bacteria in Heterorhabditis nematodes that allow the worms to infect and
grow within certain insect larvae are discussed, as well as the possible metabolic role of
Aeromonas and Rikenella bacteria in medicinal leech Hirudo verbana. Genetic
mechanisms that allow these mutualistic relationships to occur are discussed, including

physical structures allowing Vibrio to inhabit the squid, bacterial behavior and gene
regulation that allows for bacterial luminescence, gene expression that allows light organ
development, and the Vibrios nutritional benefits from their host squid. Gene expression
of bacteria in nematodes that increases their virulence to insect larvae hosts is also
explained through genetic mechanisms. The purpose of these explanations is to illustrate
the extent to which genetic mechanisms in symbiotic relationships can be understood and
how more investigation into these mechanisms can be used to manipulate bacterial genes.
This knowledge can then be transferred to symbioses between bacteria and humans and
manipulated to increase the quality of our health.
5. Sharma, Rashi, et al. Antibacterial resistance: Current problems and possible
solutions. Indian Journal of Medical Sciences 2005; 59 (3): 120-129.
Sharma explains antibacterial resistance as a natural evolutionary phenomenon.
The increase in bacterial resistance in recent years is explainable in part by the misuse of
antibiotic drugs and antiseptics. Already measures have been taken to try to combat
antimicrobial resistance. These include the use of less antibacterial agents and
reinforcing proper use of them. However, more solutions must be discovered and
employed to keep up with the rapid rate that resistant microbes evolve.
6. Sood, Seema, et al. Enterococcal infections and antimicrobial resistance. Indian J
Med Res 2008; 128: 111-121.
Bacteria of the genus Enterococcus have emerged in recent years as one of the
leading causes of nosocomial infections. They cause urinary tract infections, and more
serious infections like bacteremia, neonatal sepsis, and endocarditis. They are common

causes of these infections in hospitals due to their ability to survive for a long period of
time on surfaces outside of the body, but more importantly their increasing resistance to
antibiotics. Vancomycin resistant Enterococci in particular are of great concern because
Vancomycin is one of the strongest antibiotics used to treat infections and the gene for
resistance is readily transferable from bacterium to bacterium. The paper discusses the
harm associated with such resistant microorganisms.
7. Turnbaugh, Peter J., et al. An obesity-associated gut microbiome with increased
capacity for energy harvest. Nature. 2006; 444 (21): 1027-1031.
The study focuses on the functionality of the gut microbiota in regulating obesity.
Experiments have revealed that there is an altered balance of Bacteroidetes and
Firmicutes (both bacterial divisions) in obese mice. When there is an increased ratio of
Firmicutes to Bacteroidetes in the gut, the mice tend to be obese. Microbiotas with more
Firmicutes than Bacteroidetes were denoted as an obese microbiota and a more
balanced ratio were denoted a lean microbiota. The study successfully inoculated
germ-free mice with both microbiomes. Conclusions drawn from the experiment
implicate the gut inhabiting microbes as another source of obesity. An ability to
manipulate the ratio in the microbiome may help to relieve the obesity epidemic,
indicating another positive result that may be attained through understanding of the gut
microbiota.
8. Xu, Jian and Jeffrey I. Gordon. Honor thy symbionts. PNAS. 2003; 100 (18): 1045210459.

This review discusses the positive effects of the mammalian gut microbiota and
the importance of understanding this complex symbiotic relationship. The extent of the
microbiota is described as well as its metabolic functions. These functions include the
fermentation of plant polysaccharides, breaking down of oxalates, and synthesis of
specific vitamins. Gnotobiotic experiments on mice using the bacterium B.
thetaiotaomicron and their implications are discussed in detail. This bacterium aids in
polysaccharide fermentation and the development of mucosal barriers in the intestine.
Therefore B. thetaiotaomicron affects metabolism and the immune system. The gut
microbiota has the ability to signal metabolic pathways to alter our health and
metabolism. By identifying specific bacteria and their functions and the mechanisms by
which they influence their mammalian hosts it may be possible to harness these
organisms abilities to benefit our health.
Secondary Sources
9. Alves-Araujo, C. et al. Sugar utilization patterns and respire-fermentative metabolism
in the bakers yeast Torulaspora delbrueckii. Microbiology 2007; 153: 898-904.
Alves-Araujo and colleagues discuss the mechanisms by which bakers yeast ferments
and other uses that may employ this yeast.
10. Barnett, James A. Beginnings of microbiology and biochemistry: the contribution of
yeast research. Microbiology 2003; 149: 557-567.
Barnett gives an abbreviated summary of works of early scientists like Louis Pasteur and
how they contributed to the modern science of microbiology.

11. Casadevall, Arturo, et al. Passive antibody therapy for infectious diseases. Nature
Review Microbiology 2004; 2: 695-703.
Casadevall explores the advantages and disadvantages of using antibody therapy as an
alternative and in conjunction with antibiotics.
12. Cheon, JiHoon, et al. Applicability of random cloning method to analyze microbial
community in full-scale anaerobic digesters. Journal of Bioscience and
Bioengineering 2008; 106 (2): 134-140.
Cheon et al. discuss the usefulness of microbes in waste removal and the potential for
cloning these microbes so they can remove waste on a larger scale.
13. Cox, Christopher R. and Michael S. Gilmore. Native microbial colonization of
Drosophila melanogaster and its use as a model of Enterococcus faecalis
pathogenesis. Infection and Immunity 2007; 75 (4): 1565-1576.
Cox gives an explanation of the benefits of using Drosophila in studies involving
microbes and pathogenesis.
14. Gavrilescu, M. Removal of heavy metals from the environment by biosorption.
Engineering in Life Sciences 2004; 4 (3): 219-232.
Gavrilescu explains the process of biosorption, where bacteria remove toxic heavy metals
from the soil.
15. Grice, Elizabeth A, et al. A diversity profile of the human skin microbiota. Genome
Research 2008; 18: 1043-1050.

Grice analyzes the variety of microbes that inhabit our skin and their usefulness in
protection from pathogens.
16. Huff, W.E., et al. Alternatives to antibiotics: Utilization of bacteriophage to treat
colibacillosis and prevent foodborne pathogens. Poultry Science 2005; 84: 655659.
Huff et al. discuss the use of viruses that infect and kill bacteria, called bacteriophage,
and their potential for treating disease in animals and possibly humans.
17. Jain, Amita and Pratima Dixit. Multidrug resistant to extensively drug resistant
tuberculosis: What is next? J Biosci 2008; 33(4): 605-616.
Jain and Dixit discuss the increasing number of cases of drug resistant TB and the
potential for even more emerging resistance.
18. Johnston, B.L., M.D., and J.M. Conly, M.D. Community-associated methicillinresistant Staphylococcus aureus: Continuing to evolve. Can J Infect Dis Med
Microb 2008; 19 (2): 161-163.
Johnston and Conly discuss the well-known MRSA infections and the means by which
they may acquire more resistance.
19. Kikucki, Yoshitomo and Joerg Graf. Spatial and temporal population dynamics of a
naturally-occurring two-species microbial community inside the digestive tract of
the medicinal leech. Applied and Environmental Microbiology 2007; 73 (6):
1984-1991.

Kikucki explains the microbiota in the gut of the medicinal leech and how the leech can
be used as a model organism for studying the symbiosis of bacteria and their hosts.
20. Kim, Dennis. Studying host-pathogen interactions and innate immunity in
Caenorhabditis elegans. Dis Model Mech 2008; 1 (4-5): 205-208.
Kim explains the symbiosis of C. elegans and how its mutualistic microbes enhance
immunity. His study also illustrates the usefulness of this bacteria-horst relationship in
studying similar symbioses.
21. Ko, K.S. and In Chul Kong. Conditions required for the stimulation of
bioluminescent activity of the genetically engineered bacteria, P. putida mt-2
KG1206, preserved by deep-freezing. Science of the Total Environment 2009;
407: 2427-2430.
Ko and Kong discuss the potential for using P. putida as a bioindicator for heavy metal
toxins in the environment.
22. Matson, Eric, et al. Extracting DNA from the gut microbes of the termite
(Zootermopsis nevadensis). Journal of Visualized Experiments 2007: 1-2.
Matson uses DNA from microbes inhabiting the gut of the termite to study the common
symbiotic relationship.
23. Matsumiya, Yoshiki et al. Isolation and characterization of a lipid-degrading
bacterium and its application to lipid-containing wastewater treatment. Journal
of Bioscience and Bioengineering 2007; 193 (4): 325-330.
Matsumiya et al. studied the use of bacteria in removing lipid-based waste from water.

24. Visick, Karen L. Vibrio fischeri lux genes play an important role in colonization and
development of the host light organ. Journal of Bacteriology 2000; 182 (16):
4578-4586.
Visick explores the genetic basis of the symbiosis of Vibrio and the bioluminescent squid
and explains how knowledge of how the symbiosis works can be transferable to humans
and their relationships with bacteria.
Other Acknowledgements
Alexander Fleming. Wikipedia, the free encyclopedia. 2009. 23 April 2009.
< http://en.wikipedia.org/wiki/Alexander_Fleming>
Edward Jenner. Wikipedia, the free encyclopedia. 2009. 23 April 2009. <
http://en.wikipedia.org/wiki/Edward_Jenner>
Lamont, Ann. Joseph Lister: father of modern surgery. Answersingenesis.org. 1992.
23 April 2009. < http://www.answersingenesis.org/creation/v14/i2/scientists.asp>
Madigan, Michael T., John M. Martinko, Paul V. Dunlap, and David P. Clark. Biology of
Microorganisms. 12th ed. San Francisco: Pearson Education, Inc, 2009.
Robert Koch. Wikipedia, the free encyclopedia. 2009. 23 April 2009.
< http://en.wikipedia.org/wiki/Robert_Koch>

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