Acid-Adapted Genomes

Today Kaitlin Creamer ’16 of our Kenyon bacteria lab presented her sequence analysis for eight genomes of evolved E. coli strains adapted to acid. This project required next-generation sequencing, by Illumina MySeq, performed at Michigan State where our collaborators Rich Lenski and Zack Blount work. Kaitlin and Sean Bush ’17 installed Linux, Breseq and GATK among other things in order to piece together the genomes.

The Illumina method involves fragmenting your DNA into pieces of 250 base pairs. Each piece then gets sequenced by synthesizing DNA strands in both directions, with chemical terminators that get “read” by the machine. Then, all the millions of bits get overlapped in a giant megabase jigsaw puzzle. You can see just a fragment of it above. Each of the four DNA “letters” (nucleobases) gets a different color (red, blue, green, black). The other colors indicate regions that are suspect for various reasons.

The topmost sequence is the published “reference” genome of a typical laboratory E. coli  strain. If all the 250-mer pieces show a different base at one position, that suggests a mutation. Mutant varieties eventually get selected for or against. After 2000 generations (doublings) of E. coli, we found various strains that could grow faster than the ancestral strain; but only in acid. So now we’re testing the mutations in these strains to find out how certain genes help the acid-challenged bacteria.

This same sequencing method now churns out human genomes, bringing closer the day when  we all have our DNA immortalized in the cloud.