The following is a list of terms, facts, concepts, or theories you should be aware of with respect to our

discussions on the human microbiome. Also, recall that while the exam is not cumulative, many of the
terms and concepts that were introduced in the first half of the class are relevant to material covered in
the second half and thus may be referenced to or included in the exam.

Definitions. Be able to define or explain these terms. There may be questions that build upon a simple
definition or that require you to integrate your knowledge about multiple terms
 Biofilm
 Dental Carie
 Cariogenic
 Peridontitis
 Gingivitis
 Bacterial vaginosis
 Lactic Acid
 Bacteriocins
 Bacterial Vaginosis
 Gestational diabetes
 Preterm birth
 Mean-variance relationship
 Genomic islands
 Sebaceous gland
 Atopic dermatitis
 Opportunistic pathogens
 Volatile Organic Compounds
 Metabolomics
 Bioprospecting
 Molecular Dark Matter
 Metacommunity
 Priority Effects
 Hygiene hypothesis
 Fitness effect
 Hologenome theory
 Holobiont
 Dizygotic twin
 Monozygotic twin
 Missing microbes hypothesis

Be able to provide answers to these questions. You might see derivations of these questions.
 What is a consequence of poor dental hygiene in terms of oral microbiome abundance? Where
does this change in abundance tend to be localized?
 Who are the principal phylum-level phylotypes in the oral microbiome? Are they evenly
distributed across the oral cavity?
 What are a few advantages to studying the oral microbiome as opposed to the gut microbiome?
 How do oral microbiota modulate oral health?
 Describe the process through which biofilms for and disburse in the mouth.
 What is an example of a metabolic product of oral bacteria that can be both beneficial and
problematic for the human host?
 Give an example of a biofilm that contains human microbiota and that impacts human health?
 What is required to produce a dental carie?
 Give an example of cariogenic bacteria.
 Are cariogenic bacteria normally at high or low abundance? What factors might cause their
abundance to change?
 What causes Peridontitis? What role is played by bacteria in the development of periodontitis?
 In what ways can oral bacteria impact systemic health?
 How do genetic, microbiomic and environmental factors interact to influence health?
 What factors are known to influence oral microbiome temporal dynamics?
 How does the environment of the vagina differ from other body sites we’ve discussed?
 What are some examples of disturbances that the vaginal microbiome encounters?
 What other factors work in concert with the microbiome to contribute to host health or
disease?
 How does the vagina’s physiology impact the vaginal microbiome?
 What are the health implications of the vaginal microbiome?
 What role does lactic acid play in vaginal and reproductive health?
 What are the modes of action through which bacteriocins may impact vaginal bacteria?
 What role does Hydrogen Perioxide play in the vaginal microbiome?
 Do enterotype-like communities or states exist in the vaginal microbiome? Does the vaginal
microbiome remain in the same state over time?
 What bacterial phylotype tends to predominate a healthy vaginal microbiome?
 Give an example of a vaginal dysbiosis
 How does bacterial vaginosis impact vaginal microbiome function and vaginal physiology?
 How does the vaginal microbiome vary over time? What factors contribute to this variation?
 In what ways can the maternal microb iome impact pregnancy outcomes?
 What evidence is there to support the claim that the maternal gut microbiome contributes to
gestational diabetes?
 How does the maternal gut microbiome change over the course of pregnancy? How might these
changes impact neonatal health?
 How does microbiome diversity (richness) and interindividual variability of the microbiome
change over early life development?
 What factors influence the infant microbiome?
 How does birthing method impact the infant gut microbiome?
 Discuss ways the microbiome may be colonized in infants.
 What is an example of a form of microbiome transplantation that some new parents are
practicing to normalize microbiomes of c-section delivered babies?
 How might breastmilk impact the gut microbiome?
 Be prepared to integrate your understanding of changes in the maternal microbiome with
outcomes in the infant microbiome.
 What kinds of organisms tend to comprise the skin microbiome?
 What are some ways that sweat and sebaceous glands can impact the composition of the skin
microbiome
 In terms of community variability, which kinds of microbiomes that we’ve discussed are likely to
be the most varied over time. Be prepared to defend your argument.
 Understand which varies more: different skin communities on a person or the same kind of skin
community across people.
 What bacterium is known to associate with acne?
 Different strain of bacteria appear to differentially associate with acne. What is one explanation
for such strain-level associations?
 Give an example of a (presumed) dysbiosis of the skin microbiome.
 What is an example of a skin bacterium that can become an opportunistic pathogen?
 What is a fungus that is associated with dandruff, and how does it impact skin dryness?
 How do skin microbes contribute to body odor?
 Be able to briefly describe the kind of data that metabolomics provides and why it is useful.
 How can we impute how skin bacteria associate with the skin metabolome?
 What evidence is there in support for the hypothesis that the skin microbiome may be a useful
forensics application?
 What are metacommunities and why do they matter to the human microbiome? How might
they influence human health?
 In what ways might the built microbiome impact human health?
 Be able to describe evidence in support of the claim that building design can impact the airborne
microbiome.
 How might our understanding of the built microbiome impact the spread of pathogens in
hospitals?
 How might our understanding of the aquatic microbiome be important to human health?
 How do aquatics-related engineering designs impact the microbiomes to which humans are
exposed?
 How do the built and skin microbiomes interact?
 What health factors associate with industrialization? What covariates stratify populations based
on industrialization?
 How do nonindustrialized gut microbiomes differ from industrialized microbiomes? Consider
different aspects of community ecology properties and dynamics.
 Why is it challenging to study the effect of industrialization on the microbiome? Additionally,
why is it hard to identify the specific industrialization factors are driving observed differences in
the microbiome?
 Based upon the evidence presented in class, what factors appear to differentiate the gut
microbiomes of different human populations?
 What are some ways in which the gut microbiome may impact the fitness of mammalian hosts?
 What are some ways in which the evolution of mammals may impact the structure, diversity, or
function of the gut microbiome?
 Describe the hologenome theory of evolution.
 What is a holobiont? Specifically, what is it composed of?
 How might gut microbiomes be inherited? Is there evidence for inheritance?
 How do human gut microbiomes differ from other primates?
 Do you think dietary preference or evolutionary history may impact gut microbiome
composition more? Justify your answer.
 Describe the missing microbes hypothesis. Why might it have profound implications for our
health?