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Questions
1. How does a DNA-based analysis, such as the 16S rRNA gene analysis, differ from a cultivation-based analysis? In this chapter, the DNA-based approaches have been emphasized. What are some advantages of the cultivation-based approach?
2. More and more research groups are seeking to show that changes in the microbiota of a particular site are involved in diseases such as periodontal disease, inflammatory bowel disease, and premature birth. Critics object that showing an association is not the same as demonstrating cause and effect. In the case of the obesity study, scientists tried to do this by inoculating germfree mice with different variations of the microbiota. Clearly, this would not be possible in humans. How might you prove cause and effect in humans?
3. Infants in the first years of life are often more susceptible to certain bacterial infections than older children. How can you explain this? What function of the microbiota does this illustrate?
4. Members of the microbiota cause some quite serious diseases. How could a bacterium that normally lives in a beneficial or neutral association with its human host cause serious disease?
5. Metabolic interactions between members of the microbiota are attracting more attention because two microbes working together can increase the effectiveness of a reaction catalyzed by one of them. Consider an association between a polysaccharide-fermenting microbe and a methanogen in the colon. Consider also that the overall energy of a reaction depends on the ratio of substrate to end products for a bacterium like a polysaccharide fermenter. Can you explain why a polysaccharide fermenter and a methanogen might team up in the colon?
6. The assertion is made in this chapter that scientists now believe that transfer of DNA by conjugation in the colon is occurring across species and genus lines. Suppose you found the same type of antibiotic-resistance gene in members of two different genera. What criteria might you use to show that the gene was transferred horizontally? How might you suspect that the gene was transferred by conjugation?
7. Conventional wisdom asserts that there are no methanogens in the vaginal tract. If they were present they would probably be present at low levels. How would you use the 16S rRNA approach to find them? What modification of the approach used to find bacterial sequences would you have to make?
8. PCR combined with sequencing can provide a quick identification of bacteria. What are the limitations of this approach?
9. Resident microbiotas provide protection from colonization of some pathogenic bacteria in certain parts of the body. Describe regions of the body where normal microbiotas are protective and how they accomplish this protection.
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