Read “Metagenomic insights into the human gut resistome and the forces that shape it” by Forslund et al. and answer the following questions in a text file and deposit it into the assignment folder for Homework 5.

1) What is a resistome?  Why is it useful to think about antibiotic resistance in this context rather then focusing on individual organisms?

2) What is the authors’ explanation for the presence of antibiotic resistance genes in organisms living in diverse and remote environments in the wild?

3) Describe the “farm-to-fork” model for the selection and spread of antibiotic resistant microbes.

4) Compare and contrast the strengths and limitations of traditional phenotypic tests  with metagenomics for understanding antibiotic resistance in bacteria.  How does “functional metagenomics” attempt to overcome the weaknesses of these approaches?

5) Describe the role of gene transfer in the spread of antibiotic resistance.  Based on what you read, which method(s) of gene transfer are likely involved in spreading resistance determinants in bacteria?

6) Why were the resistance genes described by Sommer et al. (page 321) mostly different from previously known resistance genes?

7) Based on what you have read, why do you think the resistance potential of human gut microbes is significantly greater in Spain and China and significantly lower in Japan and the United States?  Support your argument with specific examples form the paper.

8) The paper suggests there are three major mechanisms for antibiotic resistance.  Can you think of three different ways a bacterium might avoid being affected by antibiotics?